pax_global_header00006660000000000000000000000064126361105210014507gustar00rootroot0000000000000052 comment=a9b162d0afdf353109aa6e9d97fc23e5421554b3 libqes-0.1.21/000077500000000000000000000000001263611052100130475ustar00rootroot00000000000000libqes-0.1.21/.gitignore000066400000000000000000000001171263611052100150360ustar00rootroot00000000000000# Editor temp files *.swp *.bak *~ # compiled build *.o *.a *.so tags version libqes-0.1.21/.gitmodules000066400000000000000000000000001263611052100152120ustar00rootroot00000000000000libqes-0.1.21/.travis.yml000066400000000000000000000015341263611052100151630ustar00rootroot00000000000000language: c env: - BUILD_TYPE=Release - BUILD_TYPE=Debug - BUILD_TYPE=Coverage compiler: - clang - gcc install: - sudo apt-get install lcov python-pip - mkdir zlib && cd zlib - wget http://zlib.net/zlib-1.2.8.tar.gz - tar xvxf zlib-1.2.8.tar.gz - cd zlib-1.2.8 - ./configure - make - sudo make install - cd ../.. - sudo pip install cpp-coveralls - git submodule update --init - mkdir build - mkdir target - cd build script: - cmake .. -DCMAKE_INSTALL_PREFIX=../target -DCMAKE_BUILD_TYPE=$BUILD_TYPE - make - ctest --verbose - make install - test -f ../target/include/qes.h - if [ $static == "TRUE" ] ; then test -f ../target/lib/libqes.a; else test -f ../target/lib/libqes.so ; fi after_success: - cd .. - if [ "$BUILD_TYPE" == "Coverage" ] ; then coveralls -e target -e test -e util -e zlib -E '.*\.h' -e build/CMakeFiles; fi libqes-0.1.21/AUTHORS000066400000000000000000000000431263611052100141140ustar00rootroot00000000000000Kevin Murray libqes-0.1.21/CMakeLists.txt000066400000000000000000000113651263611052100156150ustar00rootroot00000000000000CMAKE_MINIMUM_REQUIRED(VERSION 2.8) PROJECT(libqes C) # Append cmake-modules to module path SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules") IF (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/version") FILE(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/version" LIBQES_VERSION) ELSE() # git describe as versioning EXECUTE_PROCESS(COMMAND git describe WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} OUTPUT_VARIABLE LIBQES_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) ENDIF() ############################# ## Setup CMAKE Environment ## ############################# # Set this before you include libqes as a CMake subproject, so that we know not # to add cmake to the install rule IF (LIBQES_AS_SUBMODULE) SET(LIBQES_DONT_INSTALL True) ELSE() SET(LIBQES_DONT_INSTALL False) ENDIF() OPTION(NO_OPENMP "Disable OpenMP" False) OPTION(NO_ZLIB "Disable zlib" False) # Shortcut to enable dev compile options OPTION(DEV "Enable developer warnings") IF (DEV) SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -fsanitize=undefined") SET(CMAKE_BUILD_TYPE Coverage) ENDIF() IF (NOT CMAKE_BUILD_TYPE) SET(CMAKE_BUILD_TYPE Release) ENDIF() MESSAGE(STATUS "${CMAKE_BUILD_TYPE} build of ${PROJECT_NAME} version: ${LIBQES_VERSION}") # Set output directories SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib) SET(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib) SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin) # Include coverage module IFF out build type is Coverage to avoid bailing out # with unmet dependencies on Release builds, i.e. other peoples' computers IF (CMAKE_BUILD_TYPE STREQUAL "Coverage") INCLUDE(CodeCoverage) ENDIF() # Testing ENABLE_TESTING() # Packaging SET(CPACK_GENERATOR "TGZ;TBZ2") INCLUDE(CPack) ############################### ## Find Packages and Headers ## ############################### # Header/symbols INCLUDE(CheckSymbolExists) INCLUDE(CheckFunctionExists) INCLUDE(CheckLibraryExists) INCLUDE(CheckIncludeFiles) CHECK_SYMBOL_EXISTS(vasprintf stdio.h VASPRINTF_FOUND) CHECK_SYMBOL_EXISTS(asprintf stdio.h ASPRINTF_FOUND) CHECK_SYMBOL_EXISTS(getline stdio.h GETLINE_FOUND) CHECK_SYMBOL_EXISTS(strndup string.h STRNDUP_FOUND) IF (NOT ${NO_ZLIB}) FIND_PACKAGE(ZLIB 1.2.1 REQUIRED) CHECK_LIBRARY_EXISTS(${ZLIB_LIBRARIES} gzbuffer "" GZBUFFER_FOUND) ELSE() SET(ZLIB_FOUND FALSE) SET(GZBUFFER_FOUND FALSE) SET(ZLIB_C_FLAGS "") SET(ZLIB_LIBRARIES "") SET(ZLIB_INCLUDE_DIRS "") MESSAGE(STATUS "Building without zlib") ENDIF() IF (NOT ${NO_OPENMP}) FIND_PACKAGE(OpenMP) ELSE() SET(OPENMP_FOUND FALSE) SET(OpenMP_C_FLAGS "") MESSAGE(STATUS "Building without OpenMP") ENDIF() # Set dependency flags appropriately SET(LIBQES_DEPENDS_LIBS ${LIBQES_DEPENDS_LIBS} ${ZLIB_LIBRARIES}) SET(LIBQES_DEPENDS_INCLUDE_DIRS ${LIBQES_DEPENDS_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS}) SET(LIBQES_DEPENDS_CFLAGS ${LIBQES_DEPENDS_CFLAGS} ${ZLIB_CFLAGS} ${OpenMP_C_FLAGS}) ########################## ## Set Compiler Options ## ########################## # Set GCC-specific options IF (CMAKE_COMPILER_IS_GNUCC) SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Woverride-init -Wnormalized=id -Wlogical-op") EXECUTE_PROCESS(COMMAND ${CMAKE_C_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION) IF (${GCC_VERSION} VERSION_GREATER 4.9 OR ${GCC_VERSION} VERSION_EQUAL 4.9) SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fdiagnostics-color=always") ENDIF() ENDIF() # Set CFLAGS SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wstack-protector -Wfloat-equal") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wundef -Wpointer-arith -Wstrict-prototypes") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wmissing-prototypes -Wwrite-strings -Wredundant-decls") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wchar-subscripts -Wcomment -Wformat=2 -Wwrite-strings") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wmissing-declarations -Wredundant-decls -Wnested-externs") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wbad-function-cast -Wswitch-enum -Winit-self") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wmissing-field-initializers -Wdeclaration-after-statement") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wold-style-definition -Waddress -Wmissing-noreturn ") SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wstrict-overflow=1 -Wextra -Warray-bounds -Wall") SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${LIBQES_DEPENDS_CFLAGS} -std=gnu99 ${WEXTRA_FLAGS}") SET(CMAKE_C_FLAGS_DEBUG "-ggdb") SET(CMAKE_C_FLAGS_RELEASE "-O3") # Set include dirs INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_SOURCE_DIR}/test ${CMAKE_CURRENT_SOURCE_DIR}/test/tinytest ${LIBQES_DEPENDS_INCLUDE_DIRS} ) # Set link dirs LINK_DIRECTORIES(${CMAKE_BINARY_DIR}/lib) # Traverse to library source and tests ADD_SUBDIRECTORY(src) ADD_SUBDIRECTORY(test) libqes-0.1.21/LICENSE000066400000000000000000000772461263611052100140740ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. libqes-0.1.21/README.md000066400000000000000000000025741263611052100143360ustar00rootroot00000000000000libqes ====== A C library for various bioinformatics-y tasks. Proper docs will come in time. For now, we have reasonable test coverage under `./test/` that demonstrate the API. ###Tests: | Jenkins GNU/Linux | [![Build Status](http://biojenkins.anu.edu.au/job/libqes/badge/icon)](http://biojenkins.anu.edu.au/job/libqes/) | | ----------------- | --- | | Jenkins MinGW | [![Build Status](http://biojenkins.anu.edu.au/job/libqes-mingw/badge/icon)](http://biojenkins.anu.edu.au/job/libqes-mingw/) | | TravisCI | [![Build Status](https://travis-ci.org/kdmurray91/libqes.svg?branch=dev)](https://travis-ci.org/kdmurray91/libqes) | | Test Coverage | [![Coverage Status](https://img.shields.io/coveralls/kdmurray91/libqes.svg)](https://coveralls.io/r/kdmurray91/libqes?branch=master) | License ======= ![GPL logo](http://www.gnu.org/graphics/gplv3-127x51.png) All libqes source code is licensed under the GNU Public License version 3, or a later version at your preference. For license text, see `./gpl-3.0.txt` or [the GNU website here](http://www.gnu.org/licenses/gpl-3.0.html). The source of `tinytest`, located in `tests/tinytest`, is Copyright 2009-2012 Nick Matthewson; `tinytest` is distributed under the 3-clause BSD license. `tinytest` is hosted at [Nick's github page](https://github.com/nmathewson/tinytest). `src/crc.[ch]` are from gnulib, and are licensed under the LGPL. libqes-0.1.21/TODO.md000066400000000000000000000002621263611052100141360ustar00rootroot00000000000000KDM Todos: --------- Error handling: - write tests qes_seq: - split qes_seq_print into separate functions for FASTQ and FASTA. Also maybe allow line wrapping for FASTA. libqes-0.1.21/cmake-modules/000077500000000000000000000000001263611052100155755ustar00rootroot00000000000000libqes-0.1.21/cmake-modules/CodeCoverage.cmake000066400000000000000000000126331263611052100211320ustar00rootroot00000000000000# # 2012-01-31, Lars Bilke # - Enable Code Coverage # # 2013-09-17, Joakim Söderberg # - Added support for Clang. # - Some additional usage instructions. # # USAGE: # 1. Copy this file into your cmake modules path. # # 2. Add the following line to your CMakeLists.txt: # INCLUDE(CodeCoverage) # # 3. Set compiler flags to turn off optimization and enable coverage: # SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage") # SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage") # # 3. Use the function SETUP_TARGET_FOR_COVERAGE to create a custom make target # which runs your test executable and produces a lcov code coverage report: # Example: # SETUP_TARGET_FOR_COVERAGE( # my_coverage_target # Name for custom target. # test_driver # Name of the test driver executable that runs the tests. # # NOTE! This should always have a ZERO as exit code # # otherwise the coverage generation will not complete. # coverage # Name of output directory. # ) # # 4. Build a Debug build: # cmake -DCMAKE_BUILD_TYPE=Debug .. # make # make my_coverage_target # # # Check prereqs FIND_PROGRAM( GCOV_PATH gcov ) FIND_PROGRAM( LCOV_PATH lcov ) FIND_PROGRAM( GENHTML_PATH genhtml ) FIND_PROGRAM( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/tests) SET(CMAKE_CXX_FLAGS_COVERAGE "${CMAKE_CXX_FLAGS_DEBUG} -g -O0 --coverage -fprofile-arcs -ftest-coverage" CACHE STRING "Flags used by the C++ compiler during coverage builds." FORCE) SET(CMAKE_C_FLAGS_COVERAGE "${CMAKE_C_FLAGS_DEBUG} -g -O0 --coverage -fprofile-arcs -ftest-coverage" CACHE STRING "Flags used by the C compiler during coverage builds." FORCE) SET(CMAKE_EXE_LINKER_FLAGS_COVERAGE "" CACHE STRING "Flags used for linking binaries during coverage builds." FORCE) SET(CMAKE_SHARED_LINKER_FLAGS_COVERAGE "" CACHE STRING "Flags used by the shared libraries linker during coverage builds." FORCE) MARK_AS_ADVANCED( CMAKE_CXX_FLAGS_COVERAGE CMAKE_C_FLAGS_COVERAGE CMAKE_EXE_LINKER_FLAGS_COVERAGE CMAKE_SHARED_LINKER_FLAGS_COVERAGE ) IF(NOT GCOV_PATH) MESSAGE(FATAL_ERROR "gcov not found! Aborting...") ENDIF() # NOT GCOV_PATH IF(NOT CMAKE_COMPILER_IS_GNUCC AND NOT CMAKE_COMPILER_IS_GNUCXX) # Clang version 3.0.0 and greater now supports gcov as well. MESSAGE(WARNING "Compiler is not GNU gcc! Clang Version 3.0.0 and greater supports gcov as well, but older versions don't.") IF(NOT "${CMAKE_C_COMPILER_ID}" STREQUAL "Clang" AND NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...") ENDIF() ENDIF() # NOT CMAKE_COMPILER_IS_GNUCXX # Param _targetname The name of new the custom make target # Param _testrunner The name of the target which runs the tests. # MUST return ZERO always, even on errors. # If not, no coverage report will be created! # Param _outputname lcov output is generated as _outputname.info # HTML report is generated in _outputname/index.html # Optional fourth parameter is passed as arguments to _testrunner # Pass them in list form, e.g.: "-j;2" for -j 2 FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname _coverdir) IF(NOT LCOV_PATH) MESSAGE(FATAL_ERROR "lcov not found! Aborting...") ENDIF() # NOT LCOV_PATH IF(NOT GENHTML_PATH) MESSAGE(FATAL_ERROR "genhtml not found! Aborting...") ENDIF() # NOT GENHTML_PATH # Setup target ADD_CUSTOM_TARGET(${_targetname} # Cleanup lcov ${LCOV_PATH} --rc lcov_branch_coverage=1 --directory ${_coverdir} --zerocounters # Run tests COMMAND ${_testrunner} ${ARGV4} # Capturing lcov counters and generating report COMMAND ${LCOV_PATH} --rc lcov_branch_coverage=1 --directory ${_coverdir} --capture --output-file ${_outputname}.info COMMAND ${GENHTML_PATH} --branch-coverage -o ${_outputname} ${_outputname}.info COMMAND ${CMAKE_COMMAND} -E remove ${_outputname}.info WORKING_DIRECTORY ${CMAKE_BINARY_DIR} COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report." ) # Show info where to find the report ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD COMMAND ; COMMENT "Open ./${_outputname}/index.html in your browser to view the coverage report." ) ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE # Param _targetname The name of new the custom make target # Param _testrunner The name of the target which runs the tests # Param _outputname cobertura output is generated as _outputname.xml # Optional fourth parameter is passed as arguments to _testrunner # Pass them in list form, e.g.: "-j;2" for -j 2 FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname) IF(NOT PYTHON_EXECUTABLE) MESSAGE(FATAL_ERROR "Python not found! Aborting...") ENDIF() # NOT PYTHON_EXECUTABLE IF(NOT GCOVR_PATH) MESSAGE(FATAL_ERROR "gcovr not found! Aborting...") ENDIF() # NOT GCOVR_PATH ADD_CUSTOM_TARGET(${_targetname} # Run tests ${_testrunner} ${ARGV3} # Running gcovr COMMAND ${GCOVR_PATH} -x -r ${CMAKE_SOURCE_DIR} -e '${CMAKE_SOURCE_DIR}/tests/' -o ${_outputname}.xml WORKING_DIRECTORY ${CMAKE_BINARY_DIR} COMMENT "Running gcovr to produce Cobertura code coverage report." ) # Show info where to find the report ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD COMMAND ; COMMENT "Cobertura code coverage report saved in ${_outputname}.xml." ) ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE_COBERTURA libqes-0.1.21/cmake-modules/FindLIBQES.cmake000066400000000000000000000107111263611052100203570ustar00rootroot00000000000000# - Find libqes # Find the native libqes includes and library. # Once done this will define # # LIBQES_INCLUDE_DIRS - where to find qes.h, etc. # LIBQES_LIBRARIES - List of libraries when using libqes. # LIBQES_FOUND - True if libqes found. # # LIBQES_VERSION_STRING - The version of libqes found (x.y.z) # LIBQES_VERSION_MAJOR - The major version of libqes # LIBQES_VERSION_MINOR - The minor version of libqes # LIBQES_VERSION_PATCH - The patch version of libqes # LIBQES_VERSION_PREREL - The pre-release version of libqes # LIBQES_VERSION_GIT - The git version of libqes # # An includer may set LIBQES_ROOT to a libqes installation root to tell # this module where to look. # ============================================================================= # Copyright 2014 Kevin Murray. Adapted from FindZLIB.cmake # Licensed under the 3-clause BSD license # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions # are met: # 1. Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # 2. Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and/or other materials provided with the distribution. # 3. Neither the name of the University nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND # FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE # REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, # PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; # OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, # WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. set(_LIBQES_SEARCHES) # Search LIBQES_ROOT first if it is set. if(LIBQES_ROOT) set(_LIBQES_SEARCH_ROOT PATHS ${LIBQES_ROOT} NO_DEFAULT_PATH) list(APPEND _LIBQES_SEARCHES _LIBQES_SEARCH_ROOT) endif() # Normal search. set(_LIBQES_SEARCH_NORMAL PATHS "$ENV{PROGRAMFILES}/libqes" ) list(APPEND _LIBQES_SEARCHES _LIBQES_SEARCH_NORMAL) # Try each search configuration. foreach(search ${_LIBQES_SEARCHES}) find_path(LIBQES_INCLUDE_DIR NAMES qes.h ${${search}} PATH_SUFFIXES include) find_library(LIBQES_LIBRARY NAMES qes ${${search}} PATH_SUFFIXES lib) endforeach() mark_as_advanced(LIBQES_LIBRARY LIBQES_INCLUDE_DIR) # Handle version. Again, flogged from zlib if(LIBQES_INCLUDE_DIR AND EXISTS "${LIBQES_INCLUDE_DIR}/qes_config.h") file(STRINGS "${LIBQES_INCLUDE_DIR}/qes_config.h" LIBQES_H REGEX "^#define LIBQES_VERSION \"[^\"]*\"") string(REGEX REPLACE "^.*LIBQES_VERSION \"[Vv]?([0-9]+).*$" "\\1" LIBQES_VERSION_MAJOR "${LIBQES_H}") string(REGEX REPLACE "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.([0-9]+).*$" "\\1" LIBQES_VERSION_MINOR "${LIBQES_H}") string(REGEX REPLACE "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.[0-9]+\\.([0-9]+).*$" "\\1" LIBQES_VERSION_PATCH "${LIBQES_H}") set(LIBQES_VERSION_STRING "${LIBQES_VERSION_MAJOR}.${LIBQES_VERSION_MINOR}.${LIBQES_VERSION_PATCH}") # only append a EXTRA version if it exists: set(LIBQES_VERSION_EXTRA "") if( "${LIBQES_H}" MATCHES "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.[0-9]+\\.[0-9]+(.+)\\+git.*$") set(LIBQES_VERSION_PREREL "${CMAKE_MATCH_1}") endif() if( "${LIBQES_H}" MATCHES "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.[0-9]+\\.[0-9]+.*\\+git\\.(.+)$") set(LIBQES_VERSION_git "${CMAKE_MATCH_1}") endif() set(LIBQES_VERSION_STRING "${LIBQES_VERSION_STRING}${LIBQES_VERSION_PREREL}") endif() # handle the QUIETLY and REQUIRED arguments and set LIBQES_FOUND to TRUE if # all listed variables are TRUE include(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(LIBQES REQUIRED_VARS LIBQES_LIBRARY LIBQES_INCLUDE_DIR VERSION_VAR LIBQES_VERSION_STRING) if(LIBQES_FOUND) set(LIBQES_INCLUDE_DIRS ${LIBQES_INCLUDE_DIR}) set(LIBQES_LIBRARIES ${LIBQES_LIBRARY}) endif() libqes-0.1.21/cmake-modules/GetGitRevisionDescription.cmake000066400000000000000000000100261263611052100237040ustar00rootroot00000000000000# - Returns a version string from Git # # These functions force a re-configure on each git commit so that you can # trust the values of the variables in your build system. # # get_git_head_revision( [ ...]) # # Returns the refspec and sha hash of the current head revision # # git_describe( [ ...]) # # Returns the results of git describe on the source tree, and adjusting # the output so that it tests false if an error occurs. # # git_get_exact_tag( [ ...]) # # Returns the results of git describe --exact-match on the source tree, # and adjusting the output so that it tests false if there was no exact # matching tag. # # Requires CMake 2.6 or newer (uses the 'function' command) # # Original Author: # 2009-2010 Ryan Pavlik # http://academic.cleardefinition.com # Iowa State University HCI Graduate Program/VRAC # # Copyright Iowa State University 2009-2010. # Distributed under the Boost Software License, Version 1.0. # (See accompanying file LICENSE_1_0.txt or copy at # http://www.boost.org/LICENSE_1_0.txt) if(__get_git_revision_description) return() endif() set(__get_git_revision_description YES) # We must run the following at "include" time, not at function call time, # to find the path to this module rather than the path to a calling list file get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH) function(get_git_head_revision _refspecvar _hashvar) set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}") set(GIT_DIR "${GIT_PARENT_DIR}/.git") while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}") get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH) if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT) # We have reached the root directory, we are not in git set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE) set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE) return() endif() set(GIT_DIR "${GIT_PARENT_DIR}/.git") endwhile() # check if this is a submodule if(NOT IS_DIRECTORY ${GIT_DIR}) file(READ ${GIT_DIR} submodule) string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule}) get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH) get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE) endif() set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data") if(NOT EXISTS "${GIT_DATA}") file(MAKE_DIRECTORY "${GIT_DATA}") endif() if(NOT EXISTS "${GIT_DIR}/HEAD") return() endif() set(HEAD_FILE "${GIT_DATA}/HEAD") configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY) configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in" "${GIT_DATA}/grabRef.cmake" @ONLY) include("${GIT_DATA}/grabRef.cmake") set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE) set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE) endfunction() function(git_describe _var) if(NOT GIT_FOUND) find_package(Git QUIET) endif() get_git_head_revision(refspec hash) if(NOT GIT_FOUND) set(${_var} "GIT-NOTFOUND" PARENT_SCOPE) return() endif() if(NOT hash) set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE) return() endif() # TODO sanitize #if((${ARGN}" MATCHES "&&") OR # (ARGN MATCHES "||") OR # (ARGN MATCHES "\\;")) # message("Please report the following error to the project!") # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}") #endif() #message(STATUS "Arguments to execute_process: ${ARGN}") execute_process(COMMAND "${GIT_EXECUTABLE}" describe ${hash} ${ARGN} WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}" RESULT_VARIABLE res OUTPUT_VARIABLE out ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) if(NOT res EQUAL 0) set(out "${out}-${res}-NOTFOUND") endif() set(${_var} "${out}" PARENT_SCOPE) endfunction() function(git_get_exact_tag _var) git_describe(out --exact-match ${ARGN}) set(${_var} "${out}" PARENT_SCOPE) endfunction() libqes-0.1.21/cmake-modules/GetGitRevisionDescription.cmake.in000066400000000000000000000022621263611052100243140ustar00rootroot00000000000000# # Internal file for GetGitRevisionDescription.cmake # # Requires CMake 2.6 or newer (uses the 'function' command) # # Original Author: # 2009-2010 Ryan Pavlik # http://academic.cleardefinition.com # Iowa State University HCI Graduate Program/VRAC # # Copyright Iowa State University 2009-2010. # Distributed under the Boost Software License, Version 1.0. # (See accompanying file LICENSE_1_0.txt or copy at # http://www.boost.org/LICENSE_1_0.txt) set(HEAD_HASH) file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024) string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS) if(HEAD_CONTENTS MATCHES "ref") # named branch string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}") if(EXISTS "@GIT_DIR@/${HEAD_REF}") configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY) elseif(EXISTS "@GIT_DIR@/logs/${HEAD_REF}") configure_file("@GIT_DIR@/logs/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY) set(HEAD_HASH "${HEAD_REF}") endif() else() # detached HEAD configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY) endif() if(NOT HEAD_HASH) file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024) string(STRIP "${HEAD_HASH}" HEAD_HASH) endif() libqes-0.1.21/cmake-modules/GitSemVer.cmake000066400000000000000000000033701263611052100204470ustar00rootroot00000000000000# Copyright (c) 2014-2015 Kevin Murray # # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including # without limitation the rights to use, copy, modify, merge, publish, # distribute, sublicense, and/or sell copies of the Software, and to # permit persons to whom the Software is furnished to do so, subject to # the following conditions: # # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. INCLUDE(GetGitRevisionDescription) function(GetGitSemVer _var) get_git_head_revision(rev hash) git_get_exact_tag(tag) IF(NOT "${tag}" MATCHES "^-") SET(vers "${tag}") ELSE() git_describe(gitdesc "--always") if("${gitdesc}" MATCHES "^.+-.+-.+$") STRING (REGEX REPLACE "-" " " gdlist ${gitdesc}) SEPARATE_ARGUMENTS(gdlist) LIST(GET gdlist 0 tag) LIST(GET gdlist 1 cmts_since_tag) SET(vers "${tag}-${cmts_since_tag}-dirty") ELSE() SET(vers "dirty") ENDIF() ENDIF() IF (NOT "${hash}" STREQUAL "") STRING(SUBSTRING ${hash} 0 7 hash) set(vers "${vers}+git=${hash}") ENDIF() set(${_var} ${vers} PARENT_SCOPE) endfunction() libqes-0.1.21/src/000077500000000000000000000000001263611052100136365ustar00rootroot00000000000000libqes-0.1.21/src/CMakeLists.txt000066400000000000000000000012331263611052100163750ustar00rootroot00000000000000file(GLOB LIBQES_SOURCES qes_*.c) # Targets ADD_LIBRARY(qes_static STATIC ${LIBQES_SOURCES}) SET_TARGET_PROPERTIES(qes_static PROPERTIES OUTPUT_NAME qes) TARGET_LINK_LIBRARIES(qes_static ${LIBQES_DEPENDS_LIBS}) ADD_LIBRARY(qes SHARED ${LIBQES_SOURCES}) SET_TARGET_PROPERTIES(qes PROPERTIES SONAME_VERSION 0 VERSION 0) TARGET_LINK_LIBRARIES(qes ${LIBQES_DEPENDS_LIBS}) CONFIGURE_FILE(qes_config.h.in ${CMAKE_BINARY_DIR}/qes_config.h) FILE(GLOB LIBQES_HEADERS ${CMAKE_SOURCE_DIR}/src/*.h ${CMAKE_BINARY_DIR}/qes_config.h) IF (NOT LIBQES_DONT_INSTALL) INSTALL(FILES ${LIBQES_HEADERS} DESTINATION "include") INSTALL(TARGETS qes qes_static DESTINATION "lib") ENDIF() libqes-0.1.21/src/crc.c000066400000000000000000000113551263611052100145560ustar00rootroot00000000000000/* crc.c -- cyclic redundancy checks Copyright (C) 2005-2006, 2009-2014 Free Software Foundation, Inc. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ /* Written by Simon Josefsson. */ #include "crc.h" /* Table of CRCs of all 8-bit messages. Generated by running code from RFC 1952 modified to print out the table. */ static const uint32_t crc32_table[256] = { 0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f, 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988, 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91, 0x1db71064, 0x6ab020f2, 0xf3b97148, 0x84be41de, 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7, 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9, 0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172, 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b, 0x35b5a8fa, 0x42b2986c, 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59, 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423, 0xcfba9599, 0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924, 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190, 0x01db7106, 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433, 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818, 0x7f6a0dbb, 0x086d3d2d, 0x91646c97, 0xe6635c01, 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e, 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950, 0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65, 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2, 0x4adfa541, 0x3dd895d7, 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0, 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa, 0xbe0b1010, 0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f, 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17, 0x2eb40d81, 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a, 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683, 0xe3630b12, 0x94643b84, 0x0d6d6a3e, 0x7a6a5aa8, 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1, 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb, 0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc, 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5, 0xd6d6a3e8, 0xa1d1937e, 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b, 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55, 0x316e8eef, 0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236, 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe, 0xb2bd0b28, 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d, 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a, 0x9c0906a9, 0xeb0e363f, 0x72076785, 0x05005713, 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38, 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242, 0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777, 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c, 0x8f659eff, 0xf862ae69, 0x616bffd3, 0x166ccf45, 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2, 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc, 0x40df0b66, 0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9, 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605, 0xcdd70693, 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94, 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d }; /* * The following function was extracted from RFC 1952 by Simon * Josefsson. It was modified to avoid initial and final XOR, to use * size_t for the buffer length, and to use the const keyword. */ uint32_t crc32_update_no_xor (uint32_t crc, const char *buf, size_t len) { size_t n; for (n = 0; n < len; n++) crc = crc32_table[(crc ^ buf[n]) & 0xff] ^ (crc >> 8); return crc; } uint32_t crc32_no_xor (const char *buf, size_t len) { return crc32_update_no_xor (0L, buf, len); } uint32_t crc32_update (uint32_t crc, const char *buf, size_t len) { return crc32_update_no_xor (crc ^ 0xffffffff, buf, len) ^ 0xffffffff; } uint32_t crc32 (const char *buf, size_t len) { return crc32_update (0L, buf, len); } libqes-0.1.21/src/crc.h000066400000000000000000000036131263611052100145610ustar00rootroot00000000000000/* crc.h -- cyclic redundancy checks Copyright (C) 2005, 2009-2014 Free Software Foundation, Inc. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ /* Written by Simon Josefsson. */ #ifndef CRC_H # define CRC_H 1 #include #include /* Compute CRC-32 value of LEN bytes long BUF, and return it. */ uint32_t crc32 (const char *buf, size_t len); /* Incrementally update CRC-32 value CRC using LEN bytes long BUF. In the first call, use 0 as the value for CRC. Return the updated CRC-32 value. */ uint32_t crc32_update (uint32_t crc, const char *buf, size_t len); /* Compute modified-CRC-32 value of LEN bytes long BUF, and return it. The "modification" is to avoid the initial and final XOR operation. Due to historic implementation errors, this variant is sometimes used (i.e., in RFC 3961). */ uint32_t crc32_no_xor (const char *buf, size_t len); /* Incrementally update modified-CRC-32 value CRC using LEN bytes long BUF. In the first call, use 0 as the value for CRC. Return the updated modified-CRC-32 value. The "modification" is to avoid the initial and final XOR operation. Due to historic implementation errors, this variant is sometimes used (i.e., in RFC 3961). */ uint32_t crc32_update_no_xor (uint32_t crc, const char *buf, size_t len); #endif /* CRC_H */ libqes-0.1.21/src/qes.h000066400000000000000000000025001263611052100145740ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ========================================================================== * * Filename: qes.h * * Description: Some common sequence analysis stuff * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * =========================================================================== */ #ifndef LIBQES_H #define LIBQES_H /* ##### HEADER FILE INCLUDES ########################################## */ #include #include #include #include #include #include #include #endif /* LIBQES_H */ libqes-0.1.21/src/qes_compat.c000066400000000000000000000040201263611052100161310ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_compat.c * * Description: Compatibility helpers for cross-platformness * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_compat.h" #ifndef STRNDUP_FOUND char * strndup(const char *s, size_t n) { char *dest = malloc(n+1); if (dest == NULL) return NULL; strncpy(dest, s, n); dest[n] = '\0'; return dest; } #endif #ifndef VASPRINTF_FOUND int vasprintf(char **ret, const char *format, va_list args) { va_list copy; int count; va_copy(copy, args); *ret = NULL; count = vsnprintf(NULL, 0, format, args); if (count >= 0) { char *buffer = malloc(count + 1); if (buffer == NULL) { count = -1; } else if ((count = vsnprintf(buffer, count + 1, format, copy)) < 0) { free(buffer); } else { *ret = buffer; } } va_end(copy); return count; } #endif #ifndef ASPRINTF_FOUND int asprintf(char **ret, const char *format, ...) { va_list args; int count; va_start(args, format); count = vasprintf(ret, format, args); va_end(args); return(count); } #endif libqes-0.1.21/src/qes_compat.h000066400000000000000000000025621263611052100161470ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_compat.h * * Description: Compatibility helpers for cross-platformness * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_config.h" #include #include #include #ifndef STRNDUP_FOUND char *strndup(const char *s, size_t n); #endif #ifndef VASPRINTF_FOUND int vasprintf(char **ret, const char *format, va_list args); #endif #ifndef ASPRINTF_FOUND int asprintf(char **ret, const char *format, ...); #endif libqes-0.1.21/src/qes_config.h.in000066400000000000000000000054441263611052100165400ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_config.h.in * * Description: Define various things from CMake. * * Created: 15/08/14 12:09:59 * License: GPLv3+ * Compiler: gcc, clang * * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_CONFIG_H #define QES_CONFIG_H #define LIBQES_VERSION "${LIBQES_VERSION}"; #cmakedefine GETLINE_FOUND #cmakedefine STRNDUP_FOUND #cmakedefine ZLIB_FOUND #cmakedefine GZBUFFER_FOUND #cmakedefine OPENMP_FOUND #cmakedefine ASPRINTF_FOUND #cmakedefine VASPRINTF_FOUND /* Definitions to make changing fp type easy */ #ifdef ZLIB_FOUND # include # define QES_ZTYPE gzFile # define QES_ZOPEN gzopen # define QES_ZDOPEN gzdopen # define QES_ZCLOSE gzclose # define QES_ZREAD gzread # define QES_ZWRITE gzwrite # define QES_ZFLUSH(fp) gzflush(fp, Z_SYNC_FLUSH) # define QES_ZFPRINTF gzprintf # define QES_ZFPUTS gzputs # define QES_ZFPUTC gzputc # define QES_ZFGETS gzgets # define QES_ZFGETC gzgetc # define QES_ZFUNGETC gzungetc # define QES_ZERR gzerror # define QES_ZEOF gzeof #ifdef GZBUFFER_FOUND # define QES_ZBUFFER gzbuffer #endif # define QES_ZSEEK gzseek # define QES_ZTELL gztell # define QES_ZREWIND gzrewind #else # define QES_ZTYPE FILE* # define QES_ZOPEN fopen # define QES_ZCLOSE fclose # define QES_ZDOPEN fdopen # define QES_ZCLOSE fclose # define QES_ZREAD(fp, buf, ln) fread(buf, 1, ln, fp) # define QES_ZWRITE(fp, buf, ln) fwrite(buf, 1, ln, fp) # define QES_ZFLUSH fflush # define QES_ZFPRINTF fprintf # define QES_ZFPUTS(fp, s) fputs(s, fp) # define QES_ZFPUTC(fp, c) fputc(c, fp) # define QES_ZFGETS(fp, s, l) fgets(s, l, fp) # define QES_ZFGETC fgetc # define QES_ZFUNGETC fungetc # define QES_ZERR ferror # define QES_ZEOF feof # define QES_ZBUFFER(fp, sz) setvbuf(fp, NULL, _IOFBF, sz) # define QES_ZSEEK fseek # define QES_ZTELL ftell # define QES_ZREWIND rewind #endif #endif /* QES_CONFIG_H */ libqes-0.1.21/src/qes_file.c000066400000000000000000000363741263611052100156060ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_file.c * * Description: Compressed file IO * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_file.h" static int __qes_file_fill_buffer (struct qes_file *file) { ssize_t res = 0; if (!qes_file_ok(file)) { return 0; } if (file->feof || file->eof) { file->eof = 1; return EOF; } res = QES_ZREAD(file->fp, file->buffer, QES_FILEBUFFER_LEN - 1); if (res < 0) { /* Errored */ return 0; } else if (res == 0) { /* At both buffer & file EOF */ file->eof = 1; file->feof = 1; return EOF; } else if (res < (QES_FILEBUFFER_LEN) - 1) { /* At file EOF */ file->feof = 1; } file->bufiter = file->buffer; file->bufend = file->buffer + res; file->bufend[0] = '\0'; return 1; } struct qes_file * qes_file_open_ (const char *path, const char *mode, qes_errhandler_func onerr, const char *file, int line) { struct qes_file *qf = NULL; /* Error out with NULL */ if (path == NULL || mode == NULL || onerr == NULL || file == NULL) { return NULL; } /* create file struct */ qf = qes_calloc(1, sizeof(*qf)); /* Open file, handling any errors */ qf->fp = QES_ZOPEN(path, mode); if (qf->fp == NULL) { (*onerr)("Opening file %s failed:\n%s\n", file, line, path, strerror(errno)); qes_free(qf); return(NULL); } qf->mode = qes_file_guess_mode(mode); if (qf->mode == QES_FILE_MODE_UNKNOWN) { QES_ZCLOSE(qf->fp); qes_free(qf); return NULL; } qf->buffer = qes_calloc_(sizeof(*qf->buffer), QES_FILEBUFFER_LEN, onerr, file, line); if (qf->buffer == NULL) { QES_ZCLOSE(qf->fp); qes_free(qf); (*onerr)("Coudn't allocate buffer memory", file, line); return NULL; } qf->bufiter = qf->buffer; qf->buffer[0] = '\0'; qf->bufend = qf->buffer; /* init struct fields */ qf->eof = 0; qf->filepos = 0; qf->path = strndup(path, QES_MAX_FN_LEN); return(qf); } enum qes_file_mode qes_file_guess_mode (const char *mode) { if (mode[0] == 'r') { return QES_FILE_MODE_READ; } else if(mode[0] == 'w' || mode[0] == 'a') { return QES_FILE_MODE_WRITE; } return QES_FILE_MODE_UNKNOWN; } void qes_file_rewind (struct qes_file *file) { if (qes_file_ok(file)) { QES_ZSEEK(file->fp, 0, SEEK_SET); file->filepos = 0; file->eof = 0; file->feof = 0; file->bufiter = file->buffer; file->bufend = file->buffer; } } void qes_file_close_ (struct qes_file *file) { if (file != NULL) { if (file->fp != NULL) { QES_ZCLOSE(file->fp); } qes_free(file->path); qes_free(file->buffer); file->bufiter = NULL; file->bufend = NULL; qes_free(file); } } const char * qes_file_error (struct qes_file *file) { int error = 0; const char *errstr = ""; if (!qes_file_ok(file)) { /* Never return NULL, or we'll SIGSEGV printf */ return "BAD FILE"; } #ifdef ZLIB_FOUND errstr = gzerror(file->fp, &error); if (error == Z_ERRNO) { return strerror(errno); } #else error = ferror(file->fp); if (error != 0) { errstr = strerror(errno); clearerr(file->fp); } #endif return errstr; } int qes_file_readable(struct qes_file *file) { /* Here we check that reads won't fail. We refil if we need to. */ /* Can we possibly read from this file? */ if (!qes_file_ok(file) || file->mode == QES_FILE_MODE_UNKNOWN || \ file->mode == QES_FILE_MODE_WRITE || file->eof) { return 0; } /* We can read from buffer */ if (file->bufiter < file->bufend && file->bufiter[0] != '\0') { return 1; } /* Buffer needs a refil */ if (__qes_file_fill_buffer(file) != 0) { /* we either successfully refilled, or are at EOF */ return file->eof ? EOF : 1; } else { /* No, we can't read */ return 0; } } int qes_file_writable(struct qes_file *file) { /* Here we check that reads won't fail. We refil if we need to. */ /* Can we possibly read from this file? */ if (!qes_file_ok(file) || file->mode == QES_FILE_MODE_UNKNOWN || \ file->mode == QES_FILE_MODE_READ) { return 0; } /* TODO: be more rigorous here */ return 1; } int qes_file_peek(struct qes_file *file) { if (!qes_file_ok(file) || qes_file_readable(file) == 0) { return -2; } else if (file->eof) { return EOF; } return file->bufiter[0]; } int qes_file_putstr(struct qes_file *stream, const struct qes_str *str) { /* TODO: use the buffer in write mode */ return QES_ZWRITE(stream->fp, str->str, str->len); } int qes_file_puts(struct qes_file *file, const char *str) { if (!qes_file_ok(file) || !qes_file_writable(file)) { return -2; } return QES_ZFPUTS(file->fp, str); } int qes_file_putc(struct qes_file *file, const int chr) { int res = 0; if (!qes_file_ok(file) || !qes_file_writable(file)) { return -2; } res = QES_ZFPUTC(file->fp, chr); if (res != chr) { return -1; } return 1; } int qes_file_getc(struct qes_file *file) { if (!qes_file_ok(file) || qes_file_readable(file) == 0) { return -2; } if (file->eof) { return EOF; } return (file->bufiter++)[0]; } ssize_t qes_file_getuntil_realloc_(struct qes_file *file, int delim, char **bufref, size_t *sizeref, qes_errhandler_func onerr, const char *src, const int line) { size_t len = 0; size_t tocpy = 0; char *buf = NULL; char *nextbuf = NULL; char *end = NULL; size_t size = 0; int ret = 0; if (bufref == NULL || !qes_file_ok(file) || sizeref == NULL) { return -2; } if (file->eof) { return EOF; } /* store local copies to stop dereferencing every time we need them */ buf = *bufref; size = *sizeref; /* Alloc the buffer if it's NULL */ if (buf == NULL) { buf = qes_malloc_(__INIT_LINE_LEN * sizeof(*buf), onerr, src, line); size = __INIT_LINE_LEN; buf[0] = '\0'; } /* Set nextbuf AFTER we may/may not have alloced buf above * In case we error out below, we always set bufref = buf here, as * then we don't lose the memory alloced above */ *bufref = nextbuf = buf; /* Read until delim is in file->buffer, filling buffer */ while ((end = memchr(file->bufiter, delim, file->bufend - file->bufiter)) == NULL) { /* copy the remainder of the buffer */ tocpy = file->bufend - file->bufiter; len += tocpy; while (len + 1 >= size) { size = qes_roundupz(size); buf = qes_realloc_(buf, sizeof(*buf) * size, onerr, src, line); if (buf == NULL) { /* We bail out here, and *bufref is untouched. This means we * can check for errors, and free *bufref from the calling * function */ return -2; } *bufref = buf; } /* set to the correct position in the NEW buf, maybe after realloc */ nextbuf = buf + len - tocpy; memcpy(nextbuf, file->bufiter, tocpy); /* Update pointers to point to their respective heads */ nextbuf += tocpy; file->bufiter += tocpy; /* Null-terminate buf */ buf[len] = '\0'; /* file->buffer should now be empty, so fill 'er up! */ ret = __qes_file_fill_buffer(file); if (ret == 0) { /* Couln't fill, error out */ return -2; } else if (ret == EOF) { /* EOF time */ break; } } if (end != NULL) { /* We've got the delimter in the buffer */ tocpy = end + 1 - file->bufiter; /* +1 includes the delimiter */ } else if (file->bufiter < file->bufend) { /* No delimiter, but we return what we have. */ tocpy = file->bufend - file->bufiter; } else { /* Nothign left at all */ file->eof = 1; goto done; } /* we need to ensure that we still have enough room. * This happens as above */ len += tocpy; while (len + 1 >= size) { size = qes_roundupz(size + 1); buf = qes_realloc_(buf, sizeof(*buf) * size, onerr, src, line); if (buf == NULL) { /* We bail out here, and *bufref is untouched. This means we * can check for errors, and free *bufref from the calling * function */ return -2; } *bufref = buf; } nextbuf = buf + len - tocpy; memcpy(nextbuf, file->bufiter, tocpy); file->bufiter += tocpy; /* We don't bother updating nextbuf, as this was our final copy to buf */ goto done; done: /* restore/update referred values */ *bufref = buf; *sizeref = size; if (len > 0) { /* We have something to return, so return its length */ file->filepos += len; buf[len] = '\0'; return len; } else if (file->eof) { return EOF; } else { /* Shouldn't reach here! */ return -2; } } #define qes_file_getuntil_realloc(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, QES_DEFAULT_ERR_FN, \ __FILE__, __LINE__) #define qes_file_getuntil_realloc_errnil(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, errnil, __FILE__, __LINE__) #define qes_file_getuntil_realloc_errprint(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprint, __FILE__, __LINE__) #define qes_file_getuntil_realloc_errprintexit(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprintexit, __FILE__, \ __LINE__) /* === FUNCTION ============================================================= Name: qes_file_readline_realloc Description: Read a line from `file` into a `char *` pointed to by `buf`. This function has the added benefit of `realloc`-ing `buf` to the next highest base-2 power, if we run out of space. If it is realloced, `(*size)` is updated to the new buffer size. DON'T USE ON STACK BUFFERS. Returns: ssize_t set to either the length of the line copied to `*buf`, or one of -1 (EOF) or -2 (error). * ==========================================================================*/ ssize_t qes_file_readline_realloc_ (struct qes_file *file, char **buf, size_t *size, qes_errhandler_func onerr, const char *src, const int line) { return qes_file_getuntil_realloc_(file, '\n', buf, size, onerr, src, line); } #define qes_file_readline_realloc(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, QES_DEFAULT_ERR_FN, __FILE__, \ __LINE__) #define qes_file_readline_realloc_errnil(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, errnil, __FILE__, __LINE__) #define qes_file_readline_realloc_errprint(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, errprint, __FILE__, __LINE__) #define qes_file_readline_realloc_errprintexit(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, errprintexit, __FILE__, __LINE__) /*=== FUNCTION ============================================================* Name: qes_file_getuntil Parameters: struct qes_file *file: File to read const int delim: Delimiter char. Description: Reads ``file`` into ``dest`` until ``delim`` is found or ``maxlen - `` bytes have been read. ``delim`` is copied into ``dest``! ``delim`` can be EOF for "read until EOF", or any other thing that fits in a ``char``. Returns: ssize_t: EOF, -2 (error) or size of data read. *===========================================================================*/ ssize_t qes_file_getuntil (struct qes_file *file, const int delim, char *dest, size_t maxlen) { size_t len = 0; char *nextbuf = dest; size_t tocpy = 0; char *end = NULL; int ret = 0 ; if (dest == NULL || !qes_file_ok(file) || maxlen < 1 || delim > 255) { /* EOF is normally == -1, so use -2 to differentiate them */ return -2; } /* For detailed commentary, see qes_file_getuntil_realloc */ /* Get out early if we're at EOF already */ if (file->eof) { return EOF; } while ((end = memchr(file->bufiter, delim, file->bufend - file->bufiter)) == NULL) { tocpy = file->bufend - file->bufiter; if (len + tocpy >= maxlen) { /* + 1 because we always leave space for \0 */ tocpy += maxlen - (len + tocpy + 1); } len += tocpy; memcpy(nextbuf, file->bufiter, tocpy); nextbuf += tocpy; file->bufiter += tocpy; dest[len] = '\0'; /* Null-terminate buf */ ret = __qes_file_fill_buffer(file); if (ret == 0) { return -2; } else if (ret == EOF) { break; } } if (end != NULL) { tocpy = (end - file->bufiter) + 1; /* +1 includes the delimiter */ } else if (file->bufiter < file->bufend) { tocpy = file->bufend - file->bufiter; } else { /* Nothign left at all */ file->eof = 1; goto done; } if (len + tocpy >= maxlen) { /* maxlen - 1 because we always leave space for \0 */ tocpy += maxlen - (len + tocpy + 1); } memcpy(nextbuf, file->bufiter, tocpy); len += tocpy; file->bufiter += tocpy; goto done; done: if (len > 0) { file->filepos += len; dest[len] = '\0'; return len; } else if (file->eof) { return EOF; } else { return -2; } } ssize_t qes_file_readline (struct qes_file *file, char *dest, size_t maxlen) { return qes_file_getuntil(file, '\n', dest, maxlen); } ssize_t qes_file_readline_str (struct qes_file *file, struct qes_str *str) { ssize_t len = 0; if (file == NULL || !qes_str_ok(str)) { return -2; /* ERROR, not EOF */ } len = qes_file_readline_realloc(file, &(str->str), &(str->capacity)); if (len < 0) { qes_str_nullify(str); return len; } str->len = len; return len; } libqes-0.1.21/src/qes_file.h000066400000000000000000000257031263611052100156050ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_file.h * * Description: Compressed file IO * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_FILE_H #define QES_FILE_H #include #include enum qes_file_mode { QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_READ, QES_FILE_MODE_WRITE }; struct qes_file { QES_ZTYPE fp; char *path; char *buffer; char *bufiter; char *bufend; off_t filepos; enum qes_file_mode mode; /* Is the fp at EOF, AND do we have nothing left to copy from the buffer */ int eof; /* Is the fp at EOF */ int feof; }; /* qes_file_open: Create a `struct qes_file` and open `path` with mode `mode` and errorhandler `onerr` */ struct qes_file *qes_file_open_(const char *path, const char *mode, qes_errhandler_func onerr, const char *file, int line); #define qes_file_open(pth, mod) \ qes_file_open_(pth, mod, QES_DEFAULT_ERR_FN, __FILE__, __LINE__) #define qes_file_open_errnil(pth, mod) \ qes_file_open_(pth, mod, errnil, __FILE__, __LINE__) #define qes_file_open_errprint(pth, mod) \ qes_file_open_(pth, mod, errprint, __FILE__, __LINE__) #define qes_file_open_errprintexit(pth, mod) \ qes_file_open_(pth, mod, errprintexit, __FILE__, __LINE__) /*=== FUNCTION ============================================================* Name: qes_file_close Parameters: struct qes_file *file: file to close. Description: Closes the file pointer in ``file``, frees dynamically allocated members of ``file`` and sets ``file`` to NULL. Returns: void *===========================================================================*/ void qes_file_close_ (struct qes_file *file); #define qes_file_close(file) do { \ qes_file_close_ (file); \ file = NULL; \ } while(0) int qes_file_readable (struct qes_file *file); int qes_file_writable (struct qes_file *file); enum qes_file_mode qes_file_guess_mode (const char *mode); void qes_file_rewind (struct qes_file *file); int qes_file_peek (struct qes_file *file); int qes_file_putstr (struct qes_file *stream, const struct qes_str *str); int qes_file_puts (struct qes_file *file, const char *str); int qes_file_putc (struct qes_file *stream, const int chr); int qes_file_getc (struct qes_file *file); /*=== FUNCTION ============================================================* Name: qes_file_readline Parameters: struct qes_file *file: File to read char *dest: Destination buffer size_t maxlen: size of destination buffer Description: Reads at most ``maxlen - 1`` bytes of the next '\n' delimited line into ``dest``, and null- terminates ``dest``. The '\n' is copied, and therefore counts towards ``strlen()`` of ``dest``. Returns: ssize_t: EOF, -2 (error), or length of bytes copied, i.e. ``strlen(dest);`` *===========================================================================*/ ssize_t qes_file_readline (struct qes_file *file, char *dest, size_t maxlen); /*=== FUNCTION ============================================================* Name: qes_file_readline_str Parameters: struct qes_file *file: File to read. struct qes_str *str: struct qes_str object to read into. Description: Convenience wrapper around qes_file_readline_realloc, which reads a line into a struct qes_str object, passing str->str to and str->capacity to qes_file_readline_realloc. Returns: ssize_t set to either the length of the line copied to the struct qes_str, or one of -1 (EOF) or -2 (error). * ===========================================================================*/ ssize_t qes_file_readline_str (struct qes_file *file, struct qes_str *str); /*=== FUNCTION ============================================================* Name: qes_file_getuntil Parameters: struct qes_file *file: File to read const int delim: Delimiter char. Description: Reads ``file`` into ``dest`` until ``delim`` is found or ``maxlen - `` bytes have been read. ``delim`` is copied into ``dest``! ``delim`` can be EOF for "read until EOF", or any other thing that fits in a ``char``. Returns: ssize_t: EOF, -2 (error) or size of data read. *===========================================================================*/ ssize_t qes_file_getuntil (struct qes_file *file, const int delim, char *dest, size_t maxlen); /*=== FUNCTION ============================================================* Name: qes_file_getuntil_realloc Parameters: qes_file *file: File to read. int delim: Delimiter char. char **bufref: reference to a `char *` containing the buffer. Must not refer to a ``char[]`` that cannot be resized with ``realloc``. size *sizeref: Reference to a variable tracking the allocated size of the ``char *`` referred to by ``bufref``. Description: Read a string from `file` into a `char *` pointed to by `bufref` up to and inclding the character ``delim``. This function has the added benefit of `realloc`-ing `*bufref` to the next highest base-2 power, if we run out of space. If it is realloced, `(*sizeref)` is updated to the new buffer size. Returns: ssize_t set to either the length of the line copied to `*bufref`, or one of -1 (EOF) or -2 (error). *============================================================================*/ ssize_t qes_file_getuntil_realloc_ (struct qes_file *file, int delim, char **bufref, size_t *sizeref, qes_errhandler_func onerr, const char *src, const int line); #define qes_file_getuntil_realloc(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, QES_DEFAULT_ERR_FN, \ __FILE__, __LINE__) #define qes_file_getuntil_realloc_errnil(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, errnil, __FILE__, __LINE__) #define qes_file_getuntil_realloc_errprint(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprint, __FILE__, __LINE__) #define qes_file_getuntil_realloc_errprintexit(fp, dlm, buf, sz) \ qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprintexit, __FILE__, \ __LINE__) /* === FUNCTION ============================================================= Name: qes_file_readline_realloc Description: Read a line from `file` into a `char *` pointed to by `buf`. This function has the added benefit of `realloc`-ing `buf` to the next highest base-2 power, if we run out of space. If it is realloced, `(*size)` is updated to the new buffer size. DON'T USE ON STACK BUFFERS. Returns: ssize_t set to either the length of the line copied to `*buf`, or one of -1 (EOF) or -2 (error). * ==========================================================================*/ ssize_t qes_file_readline_realloc_ (struct qes_file *file, char **buf, size_t *size, qes_errhandler_func onerr, const char *src, const int line); #define qes_file_readline_realloc(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, QES_DEFAULT_ERR_FN, __FILE__, \ __LINE__) #define qes_file_readline_realloc_errnil(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, errnil, __FILE__, __LINE__) #define qes_file_readline_realloc_errprint(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, errprint, __FILE__, __LINE__) #define qes_file_readline_realloc_errprintexit(fp, buf, sz) \ qes_file_readline_realloc_(fp, buf, sz, errprintexit, __FILE__, __LINE__) const char *qes_file_error (struct qes_file *file); static inline int qes_file_ok (const struct qes_file *qf) { /* qes_file_ok just check we won't dereference NULLs, so we check pointer * NULLness for all pointers we care about in current modes. Which, unless * we're Write-only, is all of them */ return qf != NULL && \ qf->fp != NULL && \ qf->bufiter != NULL && \ qf->buffer != NULL; } #endif /* QES_FILE_H */ libqes-0.1.21/src/qes_libgnu.c000066400000000000000000000021351263611052100161330ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_libgnu.c * Description: Functions required from gnulib * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_libgnu.h" #ifndef ZLIB_FOUND # include "crc.c" #endif libqes-0.1.21/src/qes_libgnu.h000066400000000000000000000027461263611052100161500ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_libgnu.h * Description: Functions required from gnulib * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_LIBGNU_H #define QES_LIBGNU_H #include "qes_config.h" /* This file and qes_libgnu.c are designed to allow us to keep the sources of * the gnulib functions intact and in their original separate form. */ #ifndef ZLIB_FOUND # include "crc.h" #else # include /* Cast is to avoid a difference in signed-ness in the two implementations. */ # define crc32_update(c, b, l) crc32(c, (const unsigned char *)b, l) #endif #endif /* QES_LIBGNU_H */ libqes-0.1.21/src/qes_log.c000066400000000000000000000160641263611052100154420ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_log.c * * Description: Logging module of libngs2 * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_log.h" struct qes_logger * qes_logger_create(void) { return qes_calloc(1, sizeof(struct qes_logger)); } int qes_logger_init(struct qes_logger *logger, const char *name, enum qes_log_level level) { if (logger == NULL) return 1; if (name != NULL) { logger->name = strdup(name); } else if (logger->name != NULL) { free(logger->name); logger->name = NULL; } logger->level = level; return 0; } int qes_logger_add_destination_formatted(struct qes_logger *logger, FILE *stream, enum qes_log_level level, char *(*formatter)(struct qes_log_entry *entry)) { struct qes_log_destination *new = NULL; size_t new_sz = logger->n_destinations + 1; new = qes_realloc(logger->destinations, new_sz * sizeof(*logger->destinations)); if (new == NULL) { return 1; } logger->destinations = new; logger->n_destinations = new_sz; /* For ease of reference, save the ptr to the (new) final struct in * the array */ new = &new[new_sz - 1]; new->stream = stream; new->level = level; new->formatter = formatter; return 0; } void _qes_logger_destroy(struct qes_logger *logger) { if (logger != NULL) { qes_free(logger->name); qes_free(logger->destinations); qes_free(logger); } } struct qes_log_entry * qes_log_entry_create(void) { return qes_calloc(1, sizeof(struct qes_log_entry)); } int qes_log_entry_init(struct qes_log_entry *entry, enum qes_log_level level, const char *message) { if (entry == NULL || message == NULL) return -1; entry->level = level; entry->message = strdup(message); return 0; } int qes_log_entry_format_va(struct qes_log_entry *entry, enum qes_log_level level, const char *format, va_list args) { int res = 0; char *message = NULL; /* Format the error message w/ user input */ res = vasprintf(&message, format, args); if (res < 1) { /* Alloc inside vasprintf failed */ return 1; } /* Make the entry struct */ res = qes_log_entry_init(entry, level, message); free(message); return res; } int qes_log_entry_format(struct qes_log_entry *entry, enum qes_log_level level, const char *format, ...) { va_list args; int res = 0; /* Format the error message w/ user input */ va_start(args, format); res = qes_log_entry_format_va(entry, level, format, args); va_end(args); return res; } void _qes_log_entry_destroy(struct qes_log_entry *entry) { if (entry != NULL) { qes_free(entry->message); qes_free(entry); } } void qes_log_entry_clear(struct qes_log_entry *entry) { if (entry != NULL) { qes_free(entry->message); entry->level = QES_LOG_DEBUG; } } int qes_logger_write_entry(struct qes_logger *logger, struct qes_log_entry *entry) { size_t iii; int res; if (logger == NULL || entry == NULL) return 1; /* Message is to unimportant for this logger */ if (logger->level > entry->level) return 0; for (iii = 0; iii < logger->n_destinations; iii++) { char *formatted = NULL; struct qes_log_destination *dest = &logger->destinations[iii]; /* Message is to unimportant for this destination */ if (dest->level > entry->level) continue; formatted = dest->formatter(entry); if (formatted == NULL) return 1; res = fprintf(dest->stream, "%s", formatted); fflush(dest->stream); qes_free(formatted); if (res < 0) return 1; } return 0; } int qes_log_message(struct qes_logger *logger, enum qes_log_level level, const char *message) { struct qes_log_entry entry; int res = 0; res = qes_log_entry_format(&entry, level, "%s", message); if (res != 0) return res; res = qes_logger_write_entry(logger, &entry); qes_log_entry_clear(&entry); return res; } int qes_log_format(struct qes_logger *logger, enum qes_log_level level, const char *format, ...) { struct qes_log_entry entry; va_list args; int res = 0; va_start(args, format); res = qes_log_entry_format_va(&entry, level, format, args); va_end(args); if (res != 0) return res; res = qes_logger_write_entry(logger, &entry); qes_log_entry_clear(&entry); return res; } char * qes_log_formatter_plain(struct qes_log_entry *entry) { /* In the plain-text case, we just pass the message as is. */ if (entry == NULL) return NULL; if (entry->message == NULL) return NULL; return strdup(entry->message); } char * qes_log_formatter_pretty(struct qes_log_entry *entry) { char *buf = NULL; const char *colour = ANSIRST; const char *reset = ANSIRST; char marker = ' '; int res = 0; if (entry == NULL || entry->message == NULL) return NULL; if (entry->level <= QES_LOG_DEBUG) { marker = '.'; colour = ANSIBEG ATDIM FGCYN BGBLK ANSIEND; reset = ""; } else if (entry->level <= QES_LOG_INFO) { marker = '*'; colour = ANSIBEG ATNRM FGGRN BGBLK ANSIEND; } else if (entry->level <= QES_LOG_WARNING) { marker = '!'; colour = ANSIBEG ATULN FGYEL BGBLK ANSIEND; } else if (entry->level <= QES_LOG_ERROR) { marker = 'E'; colour = ANSIBEG ATBLD FGMAG BGBLK ANSIEND; } else { marker = 'F'; colour = ANSIBEG ATBLD ATBNK FGRED BGBLK ANSIEND; } res = asprintf(&buf, "%s[%c] %s%s", colour, marker, entry->message, reset); if (res > 0) { return buf; } else { return NULL; } } libqes-0.1.21/src/qes_log.h000066400000000000000000000126321263611052100154440ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_log.h * * Description: Logging module of libngs2 * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_LOG_H #define QES_LOG_H #include #include #include #define ANSIBEG "\033[" #define ANSIEND "m" #define ANSIRST ANSIBEG "0" ANSIEND #define ATNRM "0;" #define ATBLD "1;" #define ATDIM "2;" #define ATULN "3;" #define ATBNK "5;" #define ATREV "7;" #define ATHID "8;" #define FGBLK "30;" #define FGRED "31;" #define FGGRN "32;" #define FGYEL "33;" #define FGBLU "34;" #define FGMAG "35;" #define FGCYN "36;" #define FGWHT "37;" #define BGBLK "40" #define BGRED "41" #define BGGRN "42" #define BGYEL "43" #define BGBLU "44" #define BGMAG "45" #define BGCYN "46" #define BGWHT "47" enum qes_log_level { /* The idea is that the user can add values between these, if they need * to. a la Python's logging module. */ QES_LOG_DEBUG = 0, QES_LOG_INFO = 10, QES_LOG_WARNING = 20, QES_LOG_ERROR = 30, QES_LOG_FATAL = 40, }; typedef enum qes_log_level QesLogLevel; struct qes_log_entry { char *message; enum qes_log_level level; }; typedef struct qes_log_entry QesLogEntry; struct qes_log_destination { FILE *stream; enum qes_log_level level; char *(*formatter)(struct qes_log_entry *entry); }; typedef struct qes_log_destination QesLogDestination; struct qes_logger { struct qes_log_destination *destinations; size_t n_destinations; enum qes_log_level level; char *name; int lock; }; typedef struct qes_logger QesLogger; struct qes_logger *qes_logger_create(void); int qes_logger_init(struct qes_logger *logger, const char *name, enum qes_log_level level); int qes_logger_add_destination_formatted(struct qes_logger *logger, FILE *stream, enum qes_log_level level, char *(*formatter)(struct qes_log_entry *entry)); #define qes_logger_add_destination(log, stream, level) \ qes_logger_add_destination_formatted(log, stream, level, \ &qes_log_formatter_plain) void _qes_logger_destroy(struct qes_logger *logger); #define qes_logger_destroy(l) ({ _qes_logger_destroy(l); l = NULL; }) struct qes_log_entry *qes_log_entry_create(void); int qes_log_entry_init(struct qes_log_entry *entry, enum qes_log_level level, const char *message); void qes_log_entry_clear(struct qes_log_entry *entry); char *qes_log_formatter_plain(struct qes_log_entry *entry); char *qes_log_formatter_pretty(struct qes_log_entry *entry); int qes_log_entry_format(struct qes_log_entry *entry, enum qes_log_level level, const char *format, ...); int qes_log_entry_format_va(struct qes_log_entry *entry, enum qes_log_level level, const char *format, va_list args); int qes_logger_write_entry(struct qes_logger *logger, struct qes_log_entry *entry); void _qes_log_entry_destroy(struct qes_log_entry *log_entry); #define qes_log_entry_destroy(l) ({ _qes_log_entry_destroy(l); l = NULL; }) int qes_log_message(struct qes_logger *logger, enum qes_log_level level, const char *message); #ifndef NDEBUG #define qes_log_message_debug(log, msg) qes_log_message(log, QES_LOG_DEBUG, msg) #else #define qes_log_message_debug(log, msg) #endif #define qes_log_message_info(log, msg) qes_log_message(log, QES_LOG_INFO, msg) #define qes_log_message_warning(log, msg) qes_log_message(log, QES_LOG_WARNING, msg) #define qes_log_message_error(log, msg) qes_log_message(log, QES_LOG_ERROR, msg) #define qes_log_message_fatal(log, msg) qes_log_message(log, QES_LOG_FATAL, msg) int qes_log_format(struct qes_logger *logger, enum qes_log_level level, const char *format, ...); #ifndef NDEBUG #define qes_log_format_debug(log, fmt, ...) \ qes_log_format(log, QES_LOG_DEBUG, fmt, __VA_ARGS__) #else #define qes_log_format_debug(log, fmt, ...) #endif #define qes_log_format_info(log, fmt, ...) \ qes_log_format(log, QES_LOG_INFO, fmt, __VA_ARGS__) #define qes_log_format_warning(log, fmt, ...) \ qes_log_format(log, QES_LOG_WARNING, fmt, __VA_ARGS__) #define qes_log_format_error(log, fmt, ...) \ qes_log_format(log, QES_LOG_ERROR, fmt, __VA_ARGS__) #define qes_log_format_fatal(log, fmt, ...) \ qes_log_format(log, QES_LOG_FATAL, fmt, __VA_ARGS__) #endif /* QES_LOG_H */ libqes-0.1.21/src/qes_match.c000066400000000000000000000056161263611052100157560ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_match.c * * Description: Sequence matching and finding functions used in * bioinformatic tasks * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_match.h" inline int_fast32_t qes_match_hamming (const char *seq1, const char *seq2, size_t len) { int_fast32_t mismatches = 0; size_t iii = 0; /* Error out on bad arguments */ if (seq1 == NULL || seq2 == NULL) { return -1; } /* If we've been given a length of 0, we make it up ourselves */ if (len == 0) { size_t len2 = strlen(seq2); len = strlen(seq1); /* Max of len & len2 */ if (len > len2) { len = len2; } } /* Count mismatches. See comment on analogous loop in qes_match_hamming_max * for an explanation. */ while(iii < len) { if (seq2[iii] != seq1[iii]) { mismatches++; } iii++; } return mismatches; } inline int_fast32_t qes_match_hamming_max(const char *seq1, const char *seq2, size_t len, int_fast32_t max) { int_fast32_t mismatches = 0; size_t iii = 0; /* Error out on bad arguments */ if (seq1 == NULL || seq2 == NULL || max < 0) { return -1; } /* If we've been given a length of 0, we make it up ourselves */ if (len == 0) { size_t len2 = strlen(seq2); len = strlen(seq1); /* Max of len & len2 */ if (len > len2) { len = len2; } } /* We obediently go until ``len``, assuming whoever gave us ``len`` knew WTF they were doing. This makes things a bit faster, since these functions are expected to be very much inner-loop. */ while(iii < len) { /* Find mismatch count */ if (seq2[iii] != seq1[iii]) { mismatches++; } iii++; if (mismatches > max) { /* Bail out if we're over max, always cap at max + 1 */ return max + 1; } } return mismatches; } libqes-0.1.21/src/qes_match.h000066400000000000000000000055351263611052100157630ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_match.h * * Description: Sequence matching and finding functions used in * bioinformatic tasks * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_MATCH_H #define QES_MATCH_H #include /*=== FUNCTION ============================================================* Name: qes_match_hamming Parameters: const char *seq1, *seq2: Two strings to compare. size_t len: Compare ``len`` chars. If 0, guess length with strlen (may be unsafe). Description: Find the hamming distance between two strings. The strings are matched until the length of the smallest string. Returns: The hamming distance between ``seq1`` and ``seq2``, or -1 on error. *===========================================================================*/ extern int_fast32_t qes_match_hamming(const char *seq1, const char *seq2, size_t len); /*=== FUNCTION ============================================================* Name: qes_match_hamming_max Parameters: const char *seq1, *seq2: Two strings to compare. size_t len: Compare ``len`` chars. If 0, guess length with strlen (may be unsafe). int_fast32_t max: Stop counting at ``max``, return ``max + 1``. Description: Find the hamming distance between two strings. The strings are matched until the length of the smallest string, or ``len`` charachers, or until the maximum hamming distance (``max``) is reached. Returns: The hamming distance between ``seq1`` and ``seq2``, or ``max + 1`` if the hamming distance exceeds ``max``, or -1 on error. *===========================================================================*/ extern int_fast32_t qes_match_hamming_max(const char *seq1, const char *seq2, size_t len, int_fast32_t max); #endif /* QES_MATCH_H */ libqes-0.1.21/src/qes_seq.c000066400000000000000000000135761263611052100154560ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_seq.c * * Description: Sequence structures * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_seq.h" void qes_seq_init (struct qes_seq *seq) { qes_str_init(&seq->name, __INIT_LINE_LEN); qes_str_init(&seq->comment, __INIT_LINE_LEN); qes_str_init(&seq->seq, __INIT_LINE_LEN); qes_str_init(&seq->qual, __INIT_LINE_LEN); } struct qes_seq * qes_seq_create (void) { struct qes_seq *seq = qes_malloc(sizeof(*seq)); qes_str_init(&seq->name, __INIT_LINE_LEN); qes_str_init(&seq->comment, __INIT_LINE_LEN); qes_str_init(&seq->seq, __INIT_LINE_LEN); qes_str_init(&seq->qual, __INIT_LINE_LEN); return seq; } struct qes_seq * qes_seq_create_no_qual (void) { struct qes_seq *seq = qes_malloc(sizeof(*seq)); qes_str_init(&seq->name, __INIT_LINE_LEN); qes_str_init(&seq->comment, __INIT_LINE_LEN); qes_str_init(&seq->seq, __INIT_LINE_LEN); seq->qual.capacity = 0; seq->qual.len = 0; seq->qual.str = NULL; return seq; } struct qes_seq * qes_seq_create_no_qual_or_comment (void) { struct qes_seq *seq = qes_malloc(sizeof(*seq)); qes_str_init(&seq->name, __INIT_LINE_LEN); qes_str_init(&seq->seq, __INIT_LINE_LEN); seq->qual.capacity = 0; seq->qual.len = 0; seq->qual.str = NULL; seq->comment.capacity = 0; seq->comment.len = 0; seq->comment.str = NULL; return seq; } inline int qes_seq_fill_name (struct qes_seq *seqobj, const char *name, size_t len) { if (seqobj == NULL || name == NULL || len < 1) { return 1; } qes_str_fill_charptr(&seqobj->name, name, len); return 0; } inline int qes_seq_fill_comment (struct qes_seq *seqobj, const char *comment, size_t len) { if (seqobj == NULL || comment == NULL || len < 1) { return 1; } qes_str_fill_charptr(&seqobj->comment, comment, len); return 0; } inline int qes_seq_fill_seq (struct qes_seq *seqobj, const char *seq, size_t len) { if (seqobj == NULL || seq == NULL || len < 1) { return 1; } qes_str_fill_charptr(&seqobj->seq, seq, len); return 0; } inline int qes_seq_fill_qual (struct qes_seq *seqobj, const char *qual, size_t len) { if (seqobj == NULL || qual == NULL || len < 1) { return 1; } qes_str_fill_charptr(&seqobj->qual, qual, len); return 0; } inline int qes_seq_fill_header (struct qes_seq *seqobj, char *header, size_t len) { char *tmp = NULL; size_t startfrom = 0; if (seqobj == NULL || header == NULL) { return 1; } if (len < 1) { len = strlen(header); } while (isspace(header[len-1])) { header[--len] = '\0'; } tmp = memchr(header, ' ', len); startfrom = header[0] == '@' || header[0] == '>' ? 1 : 0; if (tmp != NULL) { qes_str_fill_charptr(&seqobj->name, header + startfrom, tmp - header - startfrom); qes_str_fill_charptr(&seqobj->comment, tmp + 1, 0); } else { qes_str_fill_charptr(&seqobj->name, header + startfrom, len - startfrom); qes_str_nullify(&seqobj->comment); } return 0; } inline int qes_seq_fill(struct qes_seq *seqobj, const char *name, const char *comment, const char *seq, const char *qual) { if (!qes_seq_ok(seqobj) || name == NULL || comment == NULL || seq == NULL \ || qual == NULL) { return 1; } qes_str_nullify(&seqobj->name); qes_str_nullify(&seqobj->comment); qes_str_nullify(&seqobj->seq); qes_str_nullify(&seqobj->qual); if (qes_seq_fill_name(seqobj, name, strlen(name)) != 0) return 1; if (qes_seq_fill_comment(seqobj, comment, strlen(comment)) != 0) return 1; if (qes_seq_fill_seq(seqobj, seq, strlen(seq)) != 0) return 1; if (strlen(qual) > 0 && qes_seq_fill_qual(seqobj, qual, strlen(qual)) != 0) return 1; return 0; } /*=== FUNCTION ============================================================* Name: qes_seq_destroy Parameters: struct qes_seq *: seq to destroy. Description: Deallocate and set to NULL a struct qes_seq on the heap. Returns: void. *===========================================================================*/ void qes_seq_destroy_(struct qes_seq *seq) { if (seq != NULL) { qes_str_destroy_cp(&seq->name); qes_str_destroy_cp(&seq->comment); qes_str_destroy_cp(&seq->seq); qes_str_destroy_cp(&seq->qual); qes_free(seq); } } int qes_seq_print(const struct qes_seq *seq, FILE *stream) { if (!qes_seq_ok(seq)) return 1; if (stream == NULL) return 1; if (seq->qual.len > 0) { fputc('@', stream); } else { fputc('>', stream); } fputs(seq->name.str, stream); if (seq->comment.str) { fputc(' ', stream); fputs(seq->comment.str, stream); } fputc('\n', stream); fputs(seq->seq.str, stream); fputc('\n', stream); if (seq->qual.len > 0) { fputs("+\n", stream); fputs(seq->qual.str, stream); fputc('\n', stream); } fflush(stream); return 0; } libqes-0.1.21/src/qes_seq.h000066400000000000000000000165541263611052100154620ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_seq.h * * Description: Sequence structures * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_SEQ_H #define QES_SEQ_H #include #include /*--------------------------------------------------------------------------- | qes_seq module -- data structures to hold NGS sequences | ---------------------------------------------------------------------------*/ /* TYPE DEFINITIONS */ struct qes_seq { struct qes_str name; struct qes_str comment; struct qes_str seq; struct qes_str qual; }; /* PROTOTYPES */ /*=== FUNCTION ============================================================* Name: qes_seq_create Parameters: void Description: Create a ``struct qes_seq`` object on the heap, creating and initialising all members. qes_seq_create_no_X functions do not create or initialise the members in their names. Returns: struct qes_seq *: A non-null memory address on success, otherwise NULL. *===========================================================================*/ struct qes_seq *qes_seq_create (void); struct qes_seq *qes_seq_create_no_qual (void); struct qes_seq *qes_seq_create_no_qual_or_comment (void); void qes_seq_init (struct qes_seq *seq); /*=== FUNCTION ============================================================* Name: qes_seq_ok Parameters: struct qes_seq *: seq to check Description: Check if ``seq`` is a usable struct qes_seq struct. qes_seq_ok_no-X functions permit the member(s) in their names to be unusable. Returns: 1 if usable, 0 otherwise. *===========================================================================*/ static inline int qes_seq_ok (const struct qes_seq *seq) { return \ seq != NULL && \ qes_str_ok(&seq->name) && \ qes_str_ok(&seq->comment) && \ qes_str_ok(&seq->seq) && \ qes_str_ok(&seq->qual); } static inline int qes_seq_ok_no_comment (const struct qes_seq *seq) { return \ seq != NULL && \ qes_str_ok(&seq->name) && \ qes_str_ok(&seq->seq) && \ qes_str_ok(&seq->qual); } static inline int qes_seq_ok_no_qual (const struct qes_seq *seq) { return \ seq != NULL && \ qes_str_ok(&seq->name) && \ qes_str_ok(&seq->comment) && \ qes_str_ok(&seq->seq); } static inline int qes_seq_ok_no_comment_or_qual (const struct qes_seq *seq) { return \ seq != NULL && \ qes_str_ok(&seq->name) && \ qes_str_ok(&seq->seq); } static inline int qes_seq_has_comment (const struct qes_seq *seq) { return qes_seq_ok(seq) && seq->comment.len > 0; } static inline int qes_seq_has_qual (const struct qes_seq *seq) { return qes_seq_ok(seq) && seq->qual.len > 0; } static inline int qes_seq_n_bytes (const struct qes_seq *seq) { if (!qes_seq_ok(seq)) { return -1; } /* Arragned per line in a fastq */ return 1 + seq->name.len + \ (qes_seq_has_comment(seq) ? 1 + seq->comment.len : 0) + 1 + \ seq->seq.len + 1 +\ qes_seq_has_qual(seq) ? 2 + seq->qual.len + 1 : 0; } /*=== FUNCTION ============================================================* Name: qes_seq_fill_header Parameters: struct qes_seq *seqobj: Seq object that will receive the header. Description: Fills the name and comment members of a ``struct qes_seq`` from the header line of a fasta/fastq file. Returns: int: 1 on success, otherwise 0 for failure. *===========================================================================*/ extern int qes_seq_fill_header(struct qes_seq *seqobj, char *header, size_t len); /*=== FUNCTION ============================================================* Name: qes_seq_fill_X Parameters: These functions take a ``struct qes_seq``, a char array and the length of the char array as a size_t. Description: Fill a struct qes_seq's name, comment, seq or qual member from a char array. If a non-zero value is given to ``len``, it is assumed to be the length of the string, otherwise the length of the string is calculated using strlen. Returns: int: 1 on success, 0 on failure. *===========================================================================*/ extern int qes_seq_fill_name(struct qes_seq *seqobj, const char *name, size_t len); extern int qes_seq_fill_comment(struct qes_seq *seqobj, const char *comment, size_t len); extern int qes_seq_fill_seq(struct qes_seq *seqobj, const char *seq, size_t len); extern int qes_seq_fill_qual(struct qes_seq *seqobj, const char *qual, size_t len); extern int qes_seq_fill(struct qes_seq *seqobj, const char *name, const char *comment, const char *seq, const char *qual); /*=== FUNCTION ============================================================* Name: qes_seq_print Parameters: const struct qes_seq *: seq to print qes_seqfile_format_t: file format to print in. FILE *: open file stream to print to. Description: Print ``seq`` in formatted per ``format`` to ``stream``. Returns: int: 1 on success, 0 on failure. *===========================================================================*/ int qes_seq_print (const struct qes_seq *seq, FILE *stream); /*=== FUNCTION ============================================================* Name: qes_seq_destroy Parameters: struct qes_seq *: seq to destroy. Description: Deallocate and set to NULL a struct qes_seq on the heap. Returns: void. *===========================================================================*/ void qes_seq_destroy_(struct qes_seq *seq); #define qes_seq_destroy(seq) do { \ qes_seq_destroy_(seq); \ seq = NULL; \ } while(0) static inline int qes_seq_copy(struct qes_seq *dest, const struct qes_seq *src) { if (dest == src || !qes_seq_ok(dest) || !qes_seq_ok(src)) return 1; if (qes_str_copy(&dest->name, &src->name) != 0) return 1; if (qes_str_copy(&dest->comment, &src->comment) != 0) return 1; if (qes_str_copy(&dest->seq, &src->seq) != 0) return 1; if (qes_str_copy(&dest->qual, &src->qual) != 0) return 1; return 0; } #endif /* QES_SEQ_H */ libqes-0.1.21/src/qes_seqfile.c000066400000000000000000000236051263611052100163100ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_seqfile.c * * Description: qes_seqfile -- read sequences in FASTA or FASTQ format. * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_seqfile.h" static inline ssize_t read_fastq_seqfile(struct qes_seqfile *seqfile, struct qes_seq *seq) { /* Convenience macro, this happens a lot */ #define CHECK_AND_TRIM(subrec) if (len < 1) { \ goto error; \ } else { \ subrec.str[--len] = '\0'; \ subrec.len = len; \ } ssize_t len = 0; int next = '\0'; int errcode = -1; /* Fast-forward past the delimiter '@', ensuring it exists */ next = qes_file_getc(seqfile->qf); if (next == EOF) { return EOF; } else if (next != FASTQ_DELIM) { /* This ain't a fastq! WTF! */ errcode = -3; goto error; } len = qes_file_readline_str(seqfile->qf, &seqfile->scratch); if (len < 1) { /* Weird truncated file */ errcode = -3; goto error; } qes_seq_fill_header(seq, seqfile->scratch.str, seqfile->scratch.len); /* Fill the actual sequence directly */ len = qes_file_readline_str(seqfile->qf, &seq->seq); errcode = -4; CHECK_AND_TRIM(seq->seq) /* read the qual header, but don't store it. */ errcode = -5; next = qes_file_getc(seqfile->qf); if (next != FASTQ_QUAL_DELIM) { goto error; } while ((next = qes_file_getc(seqfile->qf)) != '\n') { if (next == EOF) { goto error; } } if (next != '\n') goto error; /* Fill the qual score string directly */ len = qes_file_readline_str(seqfile->qf, &seq->qual); errcode = -6; CHECK_AND_TRIM(seq->qual) if ((size_t)len != seq->seq.len) { /* Error out on different len qual/seq entries */ errcode = -7; goto error; } /* return seq/qual len */ seqfile->n_records++; return seq->seq.len; error: qes_str_nullify(&seq->name); qes_str_nullify(&seq->comment); qes_str_nullify(&seq->seq); qes_str_nullify(&seq->qual); return errcode; #undef CHECK_AND_TRIM } static inline ssize_t read_fasta_seqfile(struct qes_seqfile *seqfile, struct qes_seq *seq) { /* Convenience macro, this happens a lot */ #define CHECK_AND_TRIM(subrec) if (len < 1) { \ goto error; \ } else { \ subrec.str[--len] = '\0'; \ subrec.len = len; \ } ssize_t len = 0; int next = '\0'; /* This bit is basically a copy-paste from above */ /* Fast-forward past the delimiter '>', ensuring it exists */ next = qes_file_getc(seqfile->qf); if (next == EOF) { return EOF; } else if (next != FASTA_DELIM) { /* This ain't a fasta! WTF! */ goto error; } len = qes_file_readline_str(seqfile->qf, &seqfile->scratch); if (len < 1) { goto error; } qes_seq_fill_header(seq, seqfile->scratch.str, seqfile->scratch.len); /* we need to nullify seq, as we rely on seq.len being 0 as we enter this * while loop */ qes_str_nullify(&seq->seq); /* While the next char is not a '>', i.e. until next header line */ while ((next = qes_file_peek(seqfile->qf)) != EOF && next != FASTA_DELIM) { len = qes_file_readline(seqfile->qf, seq->seq.str + seq->seq.len, seq->seq.capacity - seq->seq.len - 1); if (len < 0) { goto error; } seq->seq.len += len - 1; seq->seq.str[seq->seq.len] = '\0'; if (seq->seq.capacity - 1 <= seq->seq.len) { seq->seq.capacity = qes_roundupz(seq->seq.capacity); seq->seq.str = qes_realloc(seq->seq.str, sizeof(*seq->seq.str) * seq->seq.capacity); if (seq->seq.str == NULL) { goto error; } } } seq->seq.str[seq->seq.len] = '\0'; /* return seq len */ seqfile->n_records++; qes_str_nullify(&seq->qual); return seq->seq.len; error: qes_str_nullify(&seq->name); qes_str_nullify(&seq->comment); qes_str_nullify(&seq->seq); qes_str_nullify(&seq->qual); return -2; #undef CHECK_AND_TRIM } ssize_t qes_seqfile_read (struct qes_seqfile *seqfile, struct qes_seq *seq) { if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) { return -2; } if (seqfile->qf->eof) { return EOF; } if (seqfile->format == FASTQ_FMT) { return read_fastq_seqfile(seqfile, seq); } else if (seqfile->format == FASTA_FMT) { return read_fasta_seqfile(seqfile, seq); } /* If we reach here, bail out with an error */ qes_str_nullify(&seq->name); qes_str_nullify(&seq->comment); qes_str_nullify(&seq->seq); qes_str_nullify(&seq->qual); return -2; } struct qes_seqfile * qes_seqfile_create (const char *path, const char *mode) { struct qes_seqfile *sf = NULL; if (path == NULL || mode == NULL) return NULL; sf = qes_calloc(1, sizeof(*sf)); sf->qf = qes_file_open(path, mode); if (sf->qf == NULL) { qes_free(sf->qf); qes_free(sf); return NULL; } qes_str_init(&sf->scratch, __INIT_LINE_LEN); sf->n_records = 0; qes_seqfile_guess_format(sf); return sf; } enum qes_seqfile_format qes_seqfile_guess_format (struct qes_seqfile *seqfile) { int first_char = '\0'; if (!qes_seqfile_ok(seqfile)) return UNKNOWN_FMT; if (!qes_file_readable(seqfile->qf)) return UNKNOWN_FMT; first_char = qes_file_peek(seqfile->qf); switch (first_char) { case FASTQ_DELIM: seqfile->format = FASTQ_FMT; return FASTQ_FMT; break; case FASTA_DELIM: seqfile->format = FASTA_FMT; return FASTA_FMT; break; default: seqfile->format = UNKNOWN_FMT; return UNKNOWN_FMT; } } void qes_seqfile_set_format (struct qes_seqfile *seqfile, enum qes_seqfile_format format) { if (!qes_seqfile_ok(seqfile)) return; seqfile->format = format; } void qes_seqfile_destroy_(struct qes_seqfile *seqfile) { if (seqfile != NULL) { qes_file_close(seqfile->qf); qes_str_destroy_cp(&seqfile->scratch); qes_free(seqfile); } } size_t qes_seqfile_format_seq(const struct qes_seq *seq, enum qes_seqfile_format fmt, char *buffer, size_t maxlen) { size_t len = 0; if (buffer == NULL || maxlen < 1) { return 0; } switch (fmt) { case FASTQ_FMT: if (!qes_seq_ok(seq)) { buffer[0] = '\0'; return 0; } len = snprintf(buffer, maxlen, "%c%s %s\n%s\n%c\n%s\n", FASTQ_DELIM, seq->name.str, seq->comment.str, seq->seq.str, FASTQ_QUAL_DELIM, seq->qual.str); return len; break; case FASTA_FMT: if (!qes_seq_ok_no_qual(seq)) { buffer[0] = '\0'; return 0; } len = snprintf(buffer, maxlen, "%c%s %s\n%s\n", FASTA_DELIM, seq->name.str, seq->comment.str, seq->seq.str); return len; break; case UNKNOWN_FMT: default: return 0; } } ssize_t qes_seqfile_write (struct qes_seqfile *seqfile, struct qes_seq *seq) { #define sf_putc_check(c) ret = QES_ZFPUTC(seqfile->qf->fp, c); \ if (ret != c) {return -2;} \ else {res_len += 1;} \ ret = 0 #define sf_puts_check(s) ret = QES_ZFPUTS(seqfile->qf->fp, s.str); \ if (ret < 0) {return -2;} \ else {res_len += s.len;} \ ret = 0 int ret = 0; ssize_t res_len = 0; if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) { return -2; } switch (seqfile->format) { case FASTA_FMT: sf_putc_check(FASTA_DELIM); sf_puts_check(seq->name); if (qes_seq_has_comment(seq)) { sf_putc_check(' '); sf_puts_check(seq->comment); } sf_putc_check('\n'); sf_puts_check(seq->seq); sf_putc_check('\n'); break; case FASTQ_FMT: sf_putc_check(FASTQ_DELIM); sf_puts_check(seq->name); if (qes_seq_has_comment(seq)) { sf_putc_check(' '); sf_puts_check(seq->comment); } sf_putc_check('\n'); sf_puts_check(seq->seq); sf_putc_check('\n'); if (qes_seq_has_qual(seq)) { sf_putc_check('+'); sf_putc_check('\n'); sf_puts_check(seq->qual); sf_putc_check('\n'); } break; case UNKNOWN_FMT: default: return -2; break; } return res_len; #undef sf_putc_check #undef sf_puts_check } libqes-0.1.21/src/qes_seqfile.h000066400000000000000000000300511263611052100163060ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_seqfile.h * * Description: qes_seqfile -- read sequences in FASTA or FASTQ format. * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_SEQFILE_H #define QES_SEQFILE_H #include #include #include /*-------------------------------------------------------------------------- | Seqfile -- seamless reading & writing of FASTA & FASTQ | ---------------------------------------------------------------------------*/ #define FASTA_DELIM '>' #define FASTQ_DELIM '@' #define FASTQ_QUAL_DELIM '+' enum qes_seqfile_format { UNKNOWN_FMT = 0, FASTA_FMT = 1, FASTQ_FMT = 2, }; struct qes_seqfile { struct qes_file *qf; size_t n_records; enum qes_seqfile_format format; /* A buffer to store misc shit in while reading. One per file to keep it re-entrant */ struct qes_str scratch; }; /*=== FUNCTION ============================================================* Name: qes_seqfile_create Parameters: const char *path: Path to open. const char *mode: Mode to pass to the fopen equivalent used. Description: Allocates structures, initialises values and opens the internal file handle. Returns: A fully usable ``struct qes_seqfile *`` or NULL. *===========================================================================*/ struct qes_seqfile *qes_seqfile_create (const char *path, const char *mode); /*=== FUNCTION ============================================================* Name: qes_seqfile_ok Parameters: const struct qes_seqfile *file: File reference to check. Description: Check a file reference ``file``, ensuring that it may be dereferenced and used. This checks if a buffer has been allocated and buffer pointers set appropriately IFF the file is opened for reading. No guarantees are given about being able to read from the file. Returns: An int evaluating to true if ``file`` is OK, otherwise false. *===========================================================================*/ static inline int qes_seqfile_ok(const struct qes_seqfile *file) { return (file != NULL && qes_file_ok(file->qf)); } /*=== FUNCTION ============================================================* Name: qes_seqfile_guess_format Parameters: struct qes_seqfile *file: File whose format we guess. Description: Guess, using qes_file_peek, the format of ``file``. This only inspects the first character, so it will be confused if the first character of the file is incorrect. Only use this at the start of a file (this is checked). Returns: The file's format as a enum qes_seqfile_format, or UNKNOWN_FMT if the file is not readable, or not a FASTA/FASTQ file. *===========================================================================*/ enum qes_seqfile_format qes_seqfile_guess_format(struct qes_seqfile *file); void qes_seqfile_set_format (struct qes_seqfile *file, enum qes_seqfile_format format); ssize_t qes_seqfile_read (struct qes_seqfile *file, struct qes_seq *seq); ssize_t qes_seqfile_write (struct qes_seqfile *file, struct qes_seq *seq); size_t qes_seqfile_format_seq(const struct qes_seq *seq, enum qes_seqfile_format fmt, char *buffer, size_t maxlen); void qes_seqfile_destroy_(struct qes_seqfile *seqfile); #define qes_seqfile_destroy(seqfile) do { \ qes_seqfile_destroy_(seqfile); \ seqfile = NULL; \ } while(0) #ifdef OPENMP_FOUND #define QES_SEQFILE_ITER_PARALLEL_SINGLE_BEGIN(fle, sq, ln, opts) \ _Pragma(STRINGIFY(omp parallel shared(fle) opts default(none))) \ { \ struct qes_seq *sq = qes_seq_create(); \ ssize_t ln = 0; \ while(1) { \ _Pragma(STRINGIFY(omp critical)) \ { \ ln = qes_seqfile_read(fle, sq); \ } \ if (ln < 0) { \ break; \ } #define QES_SEQFILE_ITER_PARALLEL_SINGLE_END(sq) \ } \ qes_seq_destroy(sq); \ } #define QES_SEQFILE_ITER_PARALLEL_PAIRED_BEGIN(fle1, fle2, sq1, sq2, ln1, ln2, opts)\ _Pragma(STRINGIFY(omp parallel shared(fle1, fle2) opts default(none))) \ { \ struct qes_seq *sq1 = qes_seq_create(); \ struct qes_seq *sq2 = qes_seq_create(); \ ssize_t ln1 = 0; \ ssize_t ln2 = 0; \ while(1) { \ _Pragma(STRINGIFY(omp critical)) \ { \ ln1 = qes_seqfile_read(fle1, sq1); \ ln2 = qes_seqfile_read(fle2, sq2); \ } \ if (ln1 < 0 || ln2 < 0) { \ break; \ } #define QES_SEQFILE_ITER_PARALLEL_PAIRED_END(sq1, sq2) \ } \ qes_seq_destroy(sq1); \ qes_seq_destroy(sq2); \ } #define QES_SEQFILE_ITER_PARALLEL_INTERLEAVED_BEGIN(fle, sq1, sq2, ln1, ln2, opts)\ _Pragma(STRINGIFY(omp parallel shared(fle) opts default(none))) \ { \ struct qes_seq *sq1 = qes_seq_create(); \ struct qes_seq *sq2 = qes_seq_create(); \ ssize_t ln1 = 0; \ ssize_t ln2 = 0; \ while(1) { \ _Pragma(STRINGIFY(omp critical)) \ { \ ln1 = qes_seqfile_read(fle, sq1); \ ln2 = qes_seqfile_read(fle, sq2); \ } \ if (ln1 < 0 || ln2 < 0) { \ break; \ } #define QES_SEQFILE_ITER_PARALLEL_INTERLEAVED_END(sq1, sq2) \ } \ qes_seq_destroy(sq1); \ qes_seq_destroy(sq2); \ } #endif /* OPENMP_FOUND */ #define QES_SEQFILE_ITER_SINGLE_BEGIN(fle, sq, ln) \ { \ struct qes_seq *sq = qes_seq_create(); \ /* TODO MUSTFIX check for null sq */ \ ssize_t ln = 0; \ while(1) { \ ln = qes_seqfile_read(fle, sq); \ if (ln < 0) { \ break; \ } #define QES_SEQFILE_ITER_SINGLE_END(sq) \ } \ qes_seq_destroy(sq); \ } #define QES_SEQFILE_ITER_PAIRED_BEGIN(fle1, fle2, sq1, sq2, ln1, ln2) \ { \ struct qes_seq *sq1 = qes_seq_create(); \ struct qes_seq *sq2 = qes_seq_create(); \ ssize_t ln1 = 0; \ ssize_t ln2 = 0; \ while(1) { \ ln1 = qes_seqfile_read(fle1, sq1); \ ln2 = qes_seqfile_read(fle2, sq2); \ if (ln1 < 0 || ln2 < 0) { \ break; \ } #define QES_SEQFILE_ITER_PAIRED_END(sq1, sq2) \ } \ qes_seq_destroy(sq1); \ qes_seq_destroy(sq2); \ } #define QES_SEQFILE_ITER_INTERLEAVED_BEGIN(fle, sq1, sq2, ln1, ln2) \ { \ struct qes_seq *sq1 = qes_seq_create(); \ struct qes_seq *sq2 = qes_seq_create(); \ ssize_t ln1 = 0; \ ssize_t ln2 = 0; \ while(1) { \ ln1 = qes_seqfile_read(fle, sq1); \ ln2 = qes_seqfile_read(fle, sq2); \ if (ln1 < 0 || ln2 < 0) { \ break; \ } #define QES_SEQFILE_ITER_INTERLEAVED_END(sq1, sq2) \ } \ qes_seq_destroy(sq1); \ qes_seq_destroy(sq2); \ } #endif /* QES_SEQFILE_H */ libqes-0.1.21/src/qes_sequtil.c000066400000000000000000000240111263611052100163360ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_sequtil.c * * Description: Sequence utility functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_sequtil.h" /* * === FUNCTION ============================================================= * Name: qes_sequtil_translate_codon * Description: translate a codon to an amino acid. * ============================================================================ */ inline int qes_sequtil_translate_codon (const char *codon) { if (codon == NULL || strnlen(codon, 4) != 3) { return -1; } if (codon[0] == 'A') { if (codon[1] == 'A') { if (codon[2] == 'A') return 'K'; else if (codon[2] == 'C') return 'N'; else if (codon[2] == 'G') return 'K'; else if (codon[2] == 'T') return 'N'; else if (codon[2] == 'U') return 'N'; } else if (codon[1] == 'C') { if (codon[2] == 'A') return 'T'; else if (codon[2] == 'C') return 'T'; else if (codon[2] == 'G') return 'T'; else if (codon[2] == 'T') return 'T'; else if (codon[2] == 'U') return 'T'; } else if (codon[1] == 'G') { if (codon[2] == 'A') return 'R'; else if (codon[2] == 'C') return 'S'; else if (codon[2] == 'G') return 'R'; else if (codon[2] == 'T') return 'S'; else if (codon[2] == 'U') return 'S'; } else if (codon[1] == 'T') { if (codon[2] == 'A') return 'I'; else if (codon[2] == 'C') return 'I'; else if (codon[2] == 'G') return 'M'; else if (codon[2] == 'T') return 'I'; else if (codon[2] == 'U') return 'I'; } else if (codon[1] == 'U') { if (codon[2] == 'A') return 'I'; else if (codon[2] == 'C') return 'I'; else if (codon[2] == 'G') return 'M'; else if (codon[2] == 'T') return 'I'; else if (codon[2] == 'U') return 'I'; } } else if (codon[0] == 'C') { if (codon[1] == 'A') { if (codon[2] == 'A') return 'Q'; else if (codon[2] == 'C') return 'H'; else if (codon[2] == 'G') return 'Q'; else if (codon[2] == 'T') return 'H'; else if (codon[2] == 'U') return 'H'; } else if (codon[1] == 'C') { if (codon[2] == 'A') return 'P'; else if (codon[2] == 'C') return 'P'; else if (codon[2] == 'G') return 'P'; else if (codon[2] == 'T') return 'P'; else if (codon[2] == 'U') return 'P'; } else if (codon[1] == 'G') { if (codon[2] == 'A') return 'R'; else if (codon[2] == 'C') return 'R'; else if (codon[2] == 'G') return 'R'; else if (codon[2] == 'T') return 'R'; else if (codon[2] == 'U') return 'R'; } else if (codon[1] == 'T') { if (codon[2] == 'A') return 'L'; else if (codon[2] == 'C') return 'L'; else if (codon[2] == 'G') return 'L'; else if (codon[2] == 'T') return 'L'; else if (codon[2] == 'U') return 'L'; } else if (codon[1] == 'U') { if (codon[2] == 'A') return 'L'; else if (codon[2] == 'C') return 'L'; else if (codon[2] == 'G') return 'L'; else if (codon[2] == 'T') return 'L'; else if (codon[2] == 'U') return 'L'; } } else if (codon[0] == 'G') { if (codon[1] == 'A') { if (codon[2] == 'A') return 'E'; else if (codon[2] == 'C') return 'D'; else if (codon[2] == 'G') return 'E'; else if (codon[2] == 'T') return 'D'; else if (codon[2] == 'U') return 'D'; } else if (codon[1] == 'C') { if (codon[2] == 'A') return 'A'; else if (codon[2] == 'C') return 'A'; else if (codon[2] == 'G') return 'A'; else if (codon[2] == 'T') return 'A'; else if (codon[2] == 'U') return 'A'; } else if (codon[1] == 'G') { if (codon[2] == 'A') return 'G'; else if (codon[2] == 'C') return 'G'; else if (codon[2] == 'G') return 'G'; else if (codon[2] == 'T') return 'G'; else if (codon[2] == 'U') return 'G'; } else if (codon[1] == 'T') { if (codon[2] == 'A') return 'V'; else if (codon[2] == 'C') return 'V'; else if (codon[2] == 'G') return 'V'; else if (codon[2] == 'T') return 'V'; else if (codon[2] == 'U') return 'V'; } else if (codon[1] == 'U') { if (codon[2] == 'A') return 'V'; else if (codon[2] == 'C') return 'V'; else if (codon[2] == 'G') return 'V'; else if (codon[2] == 'T') return 'V'; else if (codon[2] == 'U') return 'V'; } } else if (codon[0] == 'T') { if (codon[1] == 'A') { if (codon[2] == 'A') return '*'; else if (codon[2] == 'C') return 'Y'; else if (codon[2] == 'G') return '*'; else if (codon[2] == 'T') return 'Y'; else if (codon[2] == 'U') return 'Y'; } else if (codon[1] == 'C') { if (codon[2] == 'A') return 'S'; else if (codon[2] == 'C') return 'S'; else if (codon[2] == 'G') return 'S'; else if (codon[2] == 'T') return 'S'; else if (codon[2] == 'U') return 'S'; } else if (codon[1] == 'G') { if (codon[2] == 'A') return '*'; else if (codon[2] == 'C') return 'C'; else if (codon[2] == 'G') return 'W'; else if (codon[2] == 'T') return 'C'; else if (codon[2] == 'U') return 'C'; } else if (codon[1] == 'T') { if (codon[2] == 'A') return 'L'; else if (codon[2] == 'C') return 'F'; else if (codon[2] == 'G') return 'L'; else if (codon[2] == 'T') return 'F'; else if (codon[2] == 'U') return 'F'; } else if (codon[1] == 'U') { if (codon[2] == 'A') return 'L'; else if (codon[2] == 'C') return 'F'; else if (codon[2] == 'G') return 'L'; else if (codon[2] == 'T') return 'F'; else if (codon[2] == 'U') return 'F'; } } else if (codon[0] == 'U') { if (codon[1] == 'A') { if (codon[2] == 'A') return '*'; else if (codon[2] == 'C') return 'Y'; else if (codon[2] == 'G') return '*'; else if (codon[2] == 'T') return 'Y'; else if (codon[2] == 'U') return 'Y'; } else if (codon[1] == 'C') { if (codon[2] == 'A') return 'S'; else if (codon[2] == 'C') return 'S'; else if (codon[2] == 'G') return 'S'; else if (codon[2] == 'T') return 'S'; else if (codon[2] == 'U') return 'S'; } else if (codon[1] == 'G') { if (codon[2] == 'A') return '*'; else if (codon[2] == 'C') return 'C'; else if (codon[2] == 'G') return 'W'; else if (codon[2] == 'T') return 'C'; else if (codon[2] == 'U') return 'C'; } else if (codon[1] == 'T') { if (codon[2] == 'A') return 'L'; else if (codon[2] == 'C') return 'F'; else if (codon[2] == 'G') return 'L'; else if (codon[2] == 'T') return 'F'; else if (codon[2] == 'U') return 'F'; } else if (codon[1] == 'U') { if (codon[2] == 'A') return 'L'; else if (codon[2] == 'C') return 'F'; else if (codon[2] == 'G') return 'L'; else if (codon[2] == 'T') return 'F'; else if (codon[2] == 'U') return 'F'; } } return 'X'; } inline char * qes_sequtil_revcomp (const char *seq, size_t len) { size_t seqlen = strlen(seq); char *outseq = strdup(seq); seqlen = seqlen < len ? seqlen : len - 1; if (outseq[seqlen - 1] == '\n') { outseq[seqlen - 1] = '\0'; seqlen--; } qes_sequtil_revcomp_inplace(outseq, len); return outseq; } inline void qes_sequtil_revcomp_inplace (char *seq, size_t len) { size_t iii; /* Trim trailing whitespace */ while (len > 0 && isspace(seq[len - 1])) { seq[--len] = '\0'; } for (iii = 0; iii < len && seq[iii] != '\0'; iii++) { size_t endpos = len - iii - 1; char endchar = seq[endpos]; if (seq[iii] == 'a' || seq[iii] == 'A') seq[endpos] = 'T'; else if (seq[iii] == 'c' || seq[iii] == 'C') seq[endpos] = 'G'; else if (seq[iii] == 'g' || seq[iii] == 'G') seq[endpos] = 'C'; else if (seq[iii] == 't' || seq[iii] == 'T') seq[endpos] = 'A'; else seq[endpos] = 'N'; if (endchar == 'a' || endchar == 'A') seq[iii] = 'T'; else if (endchar == 'c' || endchar == 'C') seq[iii] = 'G'; else if (endchar == 'g' || endchar == 'G') seq[iii] = 'C'; else if (endchar == 't' || endchar == 'T') seq[iii] = 'A'; else seq[iii] = 'N'; } } libqes-0.1.21/src/qes_sequtil.h000066400000000000000000000024631263611052100163520ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_sequtil.h * * Description: Sequence utility functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_SEQUTIL_H #define QES_SEQUTIL_H #include extern int qes_sequtil_translate_codon(const char *codon); extern char *qes_sequtil_revcomp(const char *seq, size_t len); extern void qes_sequtil_revcomp_inplace(char *seq, size_t len); #endif /* QES_SEQUTIL_H */ libqes-0.1.21/src/qes_str.c000066400000000000000000000025621263611052100154670ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_str.c * * Description: String handling functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_str.h" void qes_str_print (const struct qes_str *str, FILE *stream) { if (qes_str_ok(str)) { fprintf(stream, "%s", str->str); } } void qes_str_destroy_cp (struct qes_str *str) { if (str != NULL) qes_free(str->str); } void qes_str_destroy (struct qes_str *str) { qes_str_destroy_cp(str); qes_free(str); } libqes-0.1.21/src/qes_str.h000066400000000000000000000125731263611052100154770ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_str.h * * Description: String handling functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_STR_H #define QES_STR_H #include struct qes_str { char *str; size_t len; size_t capacity; }; /*=== FUNCTION ============================================================* Name: qes_str_ok Parameters: const struct qes_str *str: `struct qes_str` ref to check. Description: Checks if a string is OK to use, i.e. checks that `str->str` is a valid `char` array. Returns: An `int` that evaluates to true or false. *===========================================================================*/ static inline int qes_str_ok (const struct qes_str *str) { return str != NULL && str->str != NULL && str->capacity > 0; } /*=== FUNCTION ============================================================* Name: qes_str_init Parameters: struct qes_str *str: String to initialise (normally on the stack). size_t len: Initial capacity of `struct qes_str`. Description: Initialise a `struct qes_str` (typically on the stack) with room for `len` characters. Returns: void *===========================================================================*/ static inline void qes_str_init (struct qes_str *str, size_t capacity) { if (str == NULL) return; str->len = 0; str->str = qes_calloc(capacity, sizeof(*str->str)); str->capacity = capacity; } /*=== FUNCTION ============================================================* Name: qes_str_create Parameters: size_t len: Initial capacity of `struct qes_str`. Description: Create a `struct qes_str` on the heap with room for `len` characters. Returns: `struct qes_str *` Pointer to a memory address. *===========================================================================*/ static inline struct qes_str * qes_str_create (size_t capacity) { struct qes_str *str = qes_calloc(1, sizeof(*str)); /* We don't worry about NULL here. qes_str_init will return before * derefencing and we'll return NULL below. */ qes_str_init(str, capacity); return str; } static inline int qes_str_fill_charptr (struct qes_str *str, const char *cp, size_t len) { if (str == NULL || cp == NULL) return 0; if (len == 0) { len = strlen(cp); } if (str->capacity < len + 1) { while (str->capacity < len + 1) { str->capacity = qes_roundupz(str->capacity); } str->str = qes_realloc(str->str, str->capacity * sizeof(*str->str)); } /* FIXME: check for null after realloc */ memcpy(str->str, cp, len); str->str[len] = '\0'; str->len = len; return 1; } /*=== FUNCTION ============================================================* Name: qes_str_nullify Parameters: struct qes_str *str: `struct qes_str` to nullify. Description: Invalidates a `struct qes_str` without freeing the `char []`. Returns: int: 0 on success, otherwise 1. *===========================================================================*/ static inline int qes_str_nullify (struct qes_str *str) { if (!qes_str_ok(str)) return 1; str->str[0] = '\0'; str->len = 0; return 0; } static inline int qes_str_copy (struct qes_str *dest, const struct qes_str *src) { if (!qes_str_ok(src) || dest == NULL) return 1; if (!qes_str_ok(dest)) qes_str_init(dest, src->capacity); memcpy(dest->str, src->str, src->capacity); return 0; } extern void qes_str_print (const struct qes_str *str, FILE *stream); /*=== FUNCTION ============================================================* Name: qes_str_destroy Parameters: struct qes_str *: `struct qes_str` to destroy. Description: Frees `str->str` and the struct qes_str struct itself. Returns: void *===========================================================================*/ extern void qes_str_destroy (struct qes_str *str); /*=== FUNCTION ============================================================* Name: qes_str_destroy_cp Parameters: struct qes_str *: String to destrop Description: Frees `str->str` without freeing the struct qes_str struct itself. For use on `struct qes_str`s allocated on the stack. Returns: void *===========================================================================*/ extern void qes_str_destroy_cp (struct qes_str *str); #endif /* QES_STR_H */ libqes-0.1.21/src/qes_util.c000066400000000000000000000041471263611052100156350ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: qes_util.c * * Description: Wrappers around std library functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "qes_util.h" /* Pull LIBQES_VERSION in from qes_config.h */ const char *libqes_version = LIBQES_VERSION; /* Valid non-function to pass to libqes functions */ void errnil (QES_ERRFN_ARGS) { (void) (msg); (void) (file); (void) (line); } /* Function to pass to libqes functions which prints out errors to stderr */ void errprint (QES_ERRFN_ARGS) { char msg_fmt[1<<8] = ""; va_list args; if (msg == NULL) { msg = "GENERIC ERROR WITH NO MESSAGE"; } va_start (args, line); vsnprintf(msg_fmt, 1<<8, msg, args); va_end (args); fprintf(stderr, "[%s: %d]: %s\n", file, line, msg_fmt); } /* Function to pass to libqes functions which prints out errors to stderr and calls `exit(EXIT_FAILURE)` */ void errprintexit (QES_ERRFN_ARGS) { char msg_fmt[1<<8] = ""; va_list args; if (msg == NULL) { msg = "GENERIC ERROR WITH NO MESSAGE"; } va_start (args, line); vsnprintf(msg_fmt, 1<<8, msg, args); va_end (args); fprintf(stderr, "[%s: %d]: %s\n", file, line, msg_fmt); QES_EXIT_FN(EXIT_FAILURE); } libqes-0.1.21/src/qes_util.h000066400000000000000000000155631263611052100156460ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* ============================================================================ * * Filename: qes_util.h * * Description: Wrappers around std library functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef QES_UTIL_H #define QES_UTIL_H /* ##### HEADER FILE INCLUDES ########################################## */ #include #include #include #include #include #include #include #include #include #include "qes_config.h" #include "qes_compat.h" #include "qes_libgnu.h" /* * Cross-platform bollocks. Thanks windows. */ #if defined(WIN32) || defined(_WIN32) #include #define QES_PATHSEP "\\" #else #define QES_PATHSEP "/" #include #endif /* * Misc constants */ extern const char *libqes_version; #define QES_MAX_FN_LEN (1<<16) /* Size of buffers for file IO */ #define QES_FILEBUFFER_LEN (16384) /* Starting point for allocing a char pointer. Set to slightly larger than the standard size of whatever you're reading in. */ #define __INIT_LINE_LEN (128) /* * Macro helpers from tor */ /* Expands to a syntactically valid empty statement. */ #define STMT_NIL (void)0 /* Expands to a syntactically valid empty statement, explicitly (void)ing its * argument. */ #define STMT_VOID(a) while (0) { (void)(a); } /* STMT_BEGIN and STMT_END are used to wrap blocks inside macros so that * the macro can be used as if it were a single C statement. */ #ifdef __GNUC__ #define STMT_BEGIN (void) ({ #define STMT_END }) #elif defined(sun) || defined(__sun__) #define STMT_BEGIN if (1) { #define STMT_END } else STMT_NIL #else #define STMT_BEGIN do { #define STMT_END } while (0) #endif /* This can be helpful in some macros, particularly with #pragma */ #ifndef STRINGIFY #define STRINGIFY(a) #a #endif /* * Error handling functions */ /* use the stdlib exit function by default, during testing we can #define this * to some kind of error handler if we need to. */ #ifndef QES_EXIT_FN #define QES_EXIT_FN exit #endif /* By default, we use this error handler. At compile or include time, we can * chose another more appropriate one if we need to. */ #ifndef QES_DEFAULT_ERR_FN #define QES_DEFAULT_ERR_FN errprintexit #endif #define QES_ERRFN_ARGS const char *msg, const char *file, int line, ... void errnil(QES_ERRFN_ARGS); void errprint (QES_ERRFN_ARGS); void errprintexit (QES_ERRFN_ARGS) __attribute__ ((noreturn)); typedef void (*qes_errhandler_func) (const char*, const char *, int, ...); /* qes_roundupz: * Round up a `size_t` to the next highest power of two. */ /* Flogged from http://stackoverflow.com/a/1322548 and http://graphics.stanford.edu/~seander/bithacks.html, and kseq.h */ static inline size_t qes_roundupz (size_t sz) { /* Decrement v only if v is not already a power of 2 */ /* I.e, roundup things already a power of 2 */ if ((sz & (sz - 1)) != 0) sz--; /* mask all bits below MSB to 1 */ sz |= sz>>1; sz |= sz>>2; sz |= sz>>4; sz |= sz>>8; sz |= sz>>16; #if UINTPTR_MAX == 0xffffffffffffffff /* 64-bit system */ sz |= sz>>32; #endif return sz + 1; } static inline uint32_t qes_roundup32 (uint32_t u32) { /* Roundup things already a power of 2 */ if ((u32 & (u32 - 1)) != 0) u32--; /* mask all bits below MSB to 1 */ u32 |= u32>>1; u32 |= u32>>2; u32 |= u32>>4; u32 |= u32>>8; u32 |= u32>>16; return u32 + 1; } static inline uint64_t qes_roundup64 (uint64_t u64) { /* Roundup things already a power of 2 */ if ((u64 & (u64 - 1)) != 0) u64--; /* mask all bits below MSB to 1 */ u64 |= u64>>1; u64 |= u64>>2; u64 |= u64>>4; u64 |= u64>>8; u64 |= u64>>16; u64 |= u64>>32; return u64 + 1; } /* INLINE FUNCTIONS */ /* Memory allocation/deallocation */ static inline void * qes_calloc_ (size_t n, size_t size, qes_errhandler_func onerr, const char *file, int line) { void *ret = calloc(n, size); if (ret == NULL) { (*onerr)("calloc returned NULL -- Out of memory", file, line); return NULL; } else { return ret; } } #define qes_calloc(n, sz) \ qes_calloc_(n, sz, QES_DEFAULT_ERR_FN, __FILE__, __LINE__) #define qes_calloc_errnil(n, sz) \ qes_calloc_(n, sz, errnil, __FILE__, __LINE__) #define qes_calloc_errprint(n, sz) \ qes_calloc_(n, sz, errprint, __FILE__, __LINE__) #define qes_calloc_errprintexit(n, sz) \ qes_calloc_(n, sz, errprintexit, __FILE__, __LINE__) static inline void * qes_malloc_ (size_t size, qes_errhandler_func onerr, const char *file, int line) { void *ret = malloc(size); if (ret == NULL) { (*onerr)("malloc returned NULL -- Out of memory", file, line); return NULL; } else { return ret; } } #define qes_malloc(sz) \ qes_malloc_(sz, QES_DEFAULT_ERR_FN, __FILE__, __LINE__) #define qes_malloc_errnil(sz) \ qes_malloc_(sz, errnil, __FILE__, __LINE__) #define qes_malloc_errprint(sz) \ qes_malloc_(sz, errprint, __FILE__, __LINE__) #define qes_malloc_errprintexit(sz) \ qes_malloc_(sz, errprintexit, __FILE__, __LINE__) static inline void * qes_realloc_ (void *data, size_t size, qes_errhandler_func onerr, const char *file, int line) { void *ret = realloc(data, size); if (ret == NULL) { (*onerr)("realloc returned NULL -- Out of memory", file, line); return NULL; } else { return ret; } } #define qes_realloc(ptr, sz) \ qes_realloc_(ptr, sz, QES_DEFAULT_ERR_FN, __FILE__, __LINE__) #define qes_realloc_errnil(ptr, sz) \ qes_realloc_(ptr, sz, errnil, __FILE__, __LINE__) #define qes_realloc_errprint(ptr, sz) \ qes_realloc_(ptr, sz, errprint, __FILE__, __LINE__) #define qes_realloc_errprintexit(ptr, sz) \ qes_realloc_(ptr, sz, errprintexit, __FILE__, __LINE__) #define qes_free(data) \ STMT_BEGIN \ if (data != NULL) { \ free(data); \ data = NULL; \ } \ STMT_END #endif /* QES_UTIL_H */ libqes-0.1.21/test/000077500000000000000000000000001263611052100140265ustar00rootroot00000000000000libqes-0.1.21/test/CMakeLists.txt000066400000000000000000000026141263611052100165710ustar00rootroot00000000000000## Compile tests, & set up coverage SET(COMMON_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/helpers.c) FILE(GLOB TEST_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/test*.c) SET(TEST_SRCS ${COMMON_SRCS} ${TEST_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/tinytest/tinytest.c) ADD_EXECUTABLE(test_libqes ${TEST_SRCS}) TARGET_LINK_LIBRARIES(test_libqes qes ${LIBQES_DEPENDS_LIBS}) IF (CMAKE_BUILD_TYPE STREQUAL "Coverage") SETUP_TARGET_FOR_COVERAGE(coverage test_libqes coverage src) ENDIF() ADD_TEST(NAME run_test_libqes COMMAND ${CMAKE_BINARY_DIR}/bin/test_libqes ${CMAKE_BINARY_DIR}) # Demos ADD_EXECUTABLE(log_demo ${CMAKE_CURRENT_SOURCE_DIR}/logdemo.c) TARGET_LINK_LIBRARIES(log_demo qes ${LIBQES_DEPENDS_LIBS}) ADD_TEST(NAME run_log_demo COMMAND ${CMAKE_BINARY_DIR}/bin/log_demo) # Benchmarking: ADD_EXECUTABLE(bench_libqes ${CMAKE_CURRENT_SOURCE_DIR}/benchmarks.c ${COMMON_SRCS}) TARGET_LINK_LIBRARIES(bench_libqes qes ${LIBQES_DEPENDS_LIBS}) ADD_TEST(NAME run_bench_libqes COMMAND ${CMAKE_BINARY_DIR}/bin/bench_libqes ${CMAKE_BINARY_DIR}/data/test.fastq 50 qes_seqfile_write kseq_parse_fq gnu_getline qes_seqfile_parse_fq qes_file_readline_realloc) # Copy test files over to bin dir ADD_CUSTOM_COMMAND(TARGET test_libqes COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/data ${CMAKE_BINARY_DIR}/data) libqes-0.1.21/test/benchmarks.c000066400000000000000000000200411263611052100163040ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: benchmarks.c * * Description: Some benchmarks * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include #include #include #include #include #include #ifdef ZLIB_FOUND # include #else # include # include #endif #include "helpers.h" #include "kseq.h" void bench_qes_file_readline_realloc_file(int silent); void bench_qes_file_readline_file(int silent); #ifdef GELINE_FOUND void bench_gnu_getline_file(int silent); #endif void bench_qes_seqfile_parse_fq(int silent); void bench_kseq_parse_fq(int silent); void bench_qes_seqfile_write(int silent); #ifdef OPENMP_FOUND void bench_qes_seqfile_par_iter_fq_macro(int silent); #endif #ifdef ZLIB_FOUND KSEQ_INIT(gzFile, gzread) #else KSEQ_INIT(int, read) #endif static char *infile; typedef struct __bench { const char *name; void (*fn)(int silent); } bench_t; void bench_qes_file_readline_realloc_file(int silent) { size_t bsz = 1<<4; char *buf = malloc(bsz); ssize_t len = 0; off_t flen = 0; struct qes_file *file = qes_file_open(infile, "r"); assert(buf != NULL); while ((len = qes_file_readline_realloc(file, &buf, &bsz)) != EOF) { flen += len; } if (!silent) printf("[qes_file_readline_realloc]\tFile of %lu chars\n", (long unsigned)flen); qes_file_close(file); free(buf); } void bench_qes_file_readline_file(int silent) { size_t bsz = 1<<10; char buf[bsz]; ssize_t len = 0; off_t flen = 0; struct qes_file *file = qes_file_open(infile, "r"); while ((len = qes_file_readline(file, buf, bsz)) != EOF) { flen += len; } if (!silent) printf("[qes_file_readline]\t\tFile of %lu chars\n", (long unsigned)flen); qes_file_close(file); } #ifdef GELINE_FOUND void bench_gnu_getline_file(int silent) { size_t bsz = 1<<4; char *buf = malloc(bsz); ssize_t len = 0; off_t flen = 0; FILE *file = fopen(infile, "r"); assert(buf != NULL); while ((len = getline(&buf, &bsz, file)) != EOF) { flen += len; } if (!silent) printf("[getline]\t\tFile of %lu chars\n", (long unsigned)flen); fclose(file); free(buf); } #endif #ifdef OPENMP_FOUND void bench_qes_seqfile_par_iter_fq_macro(int silent) { struct qes_seqfile *sf = qes_seqfile_create(infile, "r"); size_t total_len = 0; QES_SEQFILE_ITER_PARALLEL_SINGLE_BEGIN(sf, seq, seq_len, shared(total_len)) #pragma omp critical { total_len += seq->seq.len; } QES_SEQFILE_ITER_PARALLEL_SINGLE_END(seq) if (!silent) { printf("[qes_seqfile_iter_fq_macro] Total seq len %lu\n", (long unsigned)total_len); } qes_seqfile_destroy(sf); } #endif void bench_qes_seqfile_parse_fq(int silent) { struct qes_seq *seq = qes_seq_create(); struct qes_seqfile *sf = qes_seqfile_create(infile, "r"); ssize_t res = 0; size_t n_recs = 0; size_t seq_len = 0; while (res != EOF) { res = qes_seqfile_read(sf, seq); if (res < 1) { break; } seq_len += res; n_recs++; } if (!silent) { printf("[qes_seqfile_fq] Total seq len %lu\n", (long unsigned)seq_len); } qes_seqfile_destroy(sf); qes_seq_destroy(seq); } void bench_kseq_parse_fq(int silent) { #ifdef ZLIB_FOUND gzFile fp = gzopen(infile, "r"); #else int fp = open(infile, O_RDONLY); #endif kseq_t *seq = kseq_init(fp); ssize_t res = 0; size_t n_recs = 0; size_t seq_len = 0; while ((res = kseq_read(seq)) >= 0) { seq_len += res; n_recs++; } if (!silent) { printf("[kseq_fq] Total seq len %lu\n", (long unsigned) seq_len); } kseq_destroy(seq); #ifdef ZLIB_FOUND gzclose(fp); #else close(fp); #endif } void bench_qes_seqfile_write(int silent) { struct qes_seq *seq = qes_seq_create(); ssize_t res = 0; struct qes_seqfile *sf = NULL; char *fname = tmpnam(NULL); size_t iii = 0; /* Make a seq to write */ qes_seq_fill_name(seq, "HWI-TEST", 8); qes_seq_fill_comment(seq, "testseq 1 2 3", 13); qes_seq_fill_seq(seq, "ACTCAATT", 8); qes_seq_fill_qual(seq, "IIIIIIII", 8); /* Setup file for writing */ sf = qes_seqfile_create(fname, "wT"); qes_seqfile_set_format(sf, FASTQ_FMT); for (iii = 0; iii < 1<<11; iii++) { res += qes_seqfile_write(sf, seq); } if (!silent) { printf("[qes_seqfile_write] Total file len %lu to %s\n", (long unsigned)res, fname); } qes_seqfile_destroy(sf); qes_seq_destroy(seq); remove(fname); } static const bench_t benchmarks[] = { { "qes_file_readline", &bench_qes_file_readline_file}, { "qes_file_readline_realloc", &bench_qes_file_readline_realloc_file}, #ifdef GELINE_FOUND { "gnu_getline", &bench_gnu_getline_file}, #endif { "qes_seqfile_parse_fq", &bench_qes_seqfile_parse_fq}, #ifdef OPENMP_FOUND { "qes_seqfile_par_iter_fq_macro", &bench_qes_seqfile_par_iter_fq_macro}, #endif { "kseq_parse_fq", &bench_kseq_parse_fq}, { "qes_seqfile_write", &bench_qes_seqfile_write}, { NULL, NULL} }; int main (int argc, char *argv[]) { bench_t thisbench; clock_t start, end; size_t iii = 0; int rnds = 0; size_t nbench = 0; if (argc == 1) { fprintf(stderr, "USAGE:\nbench [ ...]\n\n"); fprintf(stderr, "\nAvalilable benchmarks are:\n"); nbench = 0; while (1) { thisbench = 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nÙãxüB‹:SÙÔg{wòŸ‰´îk»Æ”ü,ç§J ðÙ?8áßÝ63ú¯¯Ì:²ßSü—Õ©š+ß„á%Ôˆ'œkrjŠR™ù$¤‘±VËà!ºÃ²LÚ¶Ý\º Õl’h:)Lðx·•´çÿbY»¼æh£°Õö¡¢ê9²}¹‰uë/J“Ý4™]é0 0ˆR–E Ä·°'WÄMt«³‡^¯‚±ÜnzôRG;>»q)ýåI»ÿ×”è.:‹š1¡ .Âï÷Gœx°Æ€Ú&u”\p¡†Ø=&WH¼<^:´ãÛ¾©¢üùlibqes-0.1.21/test/data/test.fasta000066400000000000000000002614551263611052100167530ustar00rootroot00000000000000>HWI-ST960:105:D10GVACXX:2:1101:1122:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCAGTTTAA AGTTAACTCA TTG >HWI-ST960:105:D10GVACXX:2:1101:1229:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTGAGTTT TTGGACTGTA CAT >HWI-ST960:105:D10GVACXX:2:1101:1175:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAATTGT CACTGTTTCA CCC >HWI-ST960:105:D10GVACXX:2:1101:1175:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGTGACT CTGTTCCTGT TGT >HWI-ST960:105:D10GVACXX:2:1101:1204:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATCACAGA GCAGCAGTAT TTC >HWI-ST960:105:D10GVACXX:2:1101:1237:2239 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTACACAC GTATATGCAA TAC >HWI-ST960:105:D10GVACXX:2:1101:1123:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATAATGT GGTATTAGTC TG >HWI-ST960:105:D10GVACXX:2:1101:1155:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGCCACTG AACTAAAAAA AAA >HWI-ST960:105:D10GVACXX:2:1101:1443:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTACCAAAG TCTGAATGAT TAT >HWI-ST960:105:D10GVACXX:2:1101:1360:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCCGGCTCT GTCTCTCTCT CCC >HWI-ST960:105:D10GVACXX:2:1101:1272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCATTTA GAGGAAGGAG AA >HWI-ST960:105:D10GVACXX:2:1101:1423:2185 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGACGT CAAATTATGC CT >HWI-ST960:105:D10GVACXX:2:1101:1398:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAAAAAAA AAAGAATAAA GAA >HWI-ST960:105:D10GVACXX:2:1101:1333:2199 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATTACAA AGTTTACATC TCT >HWI-ST960:105:D10GVACXX:2:1101:1388:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTCGTCT TCCATTTCTA TTT >HWI-ST960:105:D10GVACXX:2:1101:1366:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTAT ATGCTGTGGT AG >HWI-ST960:105:D10GVACXX:2:1101:1297:2232 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATTCATGT TGATATATTT AT >HWI-ST960:105:D10GVACXX:2:1101:1374:2245 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTGTGTGT CTGAAGTAGT TGA >HWI-ST960:105:D10GVACXX:2:1101:1277:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATGTTTCA GACTTCGAGA AGC >HWI-ST960:105:D10GVACXX:2:1101:1425:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATATAC TTCACAACTC TG >HWI-ST960:105:D10GVACXX:2:1101:1601:2174 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTTTTACGT AGACGATGTG CC >HWI-ST960:105:D10GVACXX:2:1101:1581:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCAGTTGAG GAACTATTGT TTC >HWI-ST960:105:D10GVACXX:2:1101:1717:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAATCTTTG TACTGTTGAA CAA >HWI-ST960:105:D10GVACXX:2:1101:1538:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACTGTTT GTGTCAATCA TT >HWI-ST960:105:D10GVACXX:2:1101:1687:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGTCCTTC GGATCACTCA A >HWI-ST960:105:D10GVACXX:2:1101:1589:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGAGCACA AAGATGATCA AAC >HWI-ST960:105:D10GVACXX:2:1101:1611:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGAGAGT AGCTCTGTTT AT >HWI-ST960:105:D10GVACXX:2:1101:1672:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATATTTG ATACATCGGT TC >HWI-ST960:105:D10GVACXX:2:1101:1595:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTCTGACT GATGAACATA TTT >HWI-ST960:105:D10GVACXX:2:1101:1706:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGTGCAAT TAGTGCAACT GA >HWI-ST960:105:D10GVACXX:2:1101:1575:2228 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCGTTTGAGA CTCTATCTTA CCT >HWI-ST960:105:D10GVACXX:2:1101:1557:2229 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTTTTGT GTGTACTTGT CC >HWI-ST960:105:D10GVACXX:2:1101:1747:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATATACA ATTGTGGACT AC >HWI-ST960:105:D10GVACXX:2:1101:1921:2172 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTTAGA ACTCTTTTCC TA >HWI-ST960:105:D10GVACXX:2:1101:1992:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTGTTGG GGTAAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:1925:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAAGTGT GATTCTTTTG G >HWI-ST960:105:D10GVACXX:2:1101:1792:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAAAGTC ATGTCTTTGT TGT >HWI-ST960:105:D10GVACXX:2:1101:1771:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGGTGACCG AGAAATGTTT AA >HWI-ST960:105:D10GVACXX:2:1101:1915:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTCAGTCT AACTAAAGTA TT >HWI-ST960:105:D10GVACXX:2:1101:1899:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCACTAATA CAATTGTTGC TC >HWI-ST960:105:D10GVACXX:2:1101:2049:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTCTTG TACTACAGTG AT >HWI-ST960:105:D10GVACXX:2:1101:2035:2185 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATGTAGAA TTCAGAATGT CT >HWI-ST960:105:D10GVACXX:2:1101:2214:2203 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTGTACACG GCTTAATTTA TT >HWI-ST960:105:D10GVACXX:2:1101:2244:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCGGTTTGA GTGTTGCAAA TCT >HWI-ST960:105:D10GVACXX:2:1101:2185:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAACAAGGT CGTTGTAGTA TAG >HWI-ST960:105:D10GVACXX:2:1101:2067:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTCCATA GATTGTAGCC TC >HWI-ST960:105:D10GVACXX:2:1101:2032:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTGTTA GTTACGCTTT GC >HWI-ST960:105:D10GVACXX:2:1101:2011:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAATAT GATATGAAAA TCT >HWI-ST960:105:D10GVACXX:2:1101:2444:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTCCTGT GATTTGCAAT TTC >HWI-ST960:105:D10GVACXX:2:1101:2254:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCCATAAAA AGTCTCTACA AT >HWI-ST960:105:D10GVACXX:2:1101:2448:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGAAGAAA AAGATGACCA GCT >HWI-ST960:105:D10GVACXX:2:1101:2342:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATGTTCG ACTGTGAACC TTC >HWI-ST960:105:D10GVACXX:2:1101:2268:2215 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCAATATCAG AACTCGTTAT ATT >HWI-ST960:105:D10GVACXX:2:1101:2411:2223 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCGCAACTGT AGCAAGAAGA AAC >HWI-ST960:105:D10GVACXX:2:1101:2292:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTTACTT AAAGAGCCCT AAC >HWI-ST960:105:D10GVACXX:2:1101:2448:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATGAGTGT AGGCTTACTT AC >HWI-ST960:105:D10GVACXX:2:1101:2389:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCGATCT GGTTTGTAGA AC >HWI-ST960:105:D10GVACXX:2:1101:2675:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAAGTGA ACTCTGTGCG TCT >HWI-ST960:105:D10GVACXX:2:1101:2548:2190 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATCTTCT GTTGACTCAT GT >HWI-ST960:105:D10GVACXX:2:1101:2610:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAGTAT CAATTGAACT TTT >HWI-ST960:105:D10GVACXX:2:1101:2657:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATATATA TATAAATGCA GAC >HWI-ST960:105:D10GVACXX:2:1101:2576:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATATTTTT CCCACTGTGT TCT >HWI-ST960:105:D10GVACXX:2:1101:2626:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGAGAACTC TAGAAACCTG CTT >HWI-ST960:105:D10GVACXX:2:1101:2660:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTACAAT GTACTGGAAA CTT >HWI-ST960:105:D10GVACXX:2:1101:2509:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCAAACTT TATGTAAACT CT >HWI-ST960:105:D10GVACXX:2:1101:2536:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATACCAA ATAGAATTTC TG >HWI-ST960:105:D10GVACXX:2:1101:2584:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTGTGCCT GGATTAATAT GA >HWI-ST960:105:D10GVACXX:2:1101:2674:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGCAACT GCAAATTCTG CA >HWI-ST960:105:D10GVACXX:2:1101:2718:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACGGAACC AGTGACCGTC GT >HWI-ST960:105:D10GVACXX:2:1101:2630:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTACTTGA ACAGGATCTG TT >HWI-ST960:105:D10GVACXX:2:1101:2869:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTCCGATG ATGATCAAAT CAT >HWI-ST960:105:D10GVACXX:2:1101:2917:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGTCTCG CTTATGACTA TGA >HWI-ST960:105:D10GVACXX:2:1101:2789:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATATTGGT CTGTATTGTG CTC >HWI-ST960:105:D10GVACXX:2:1101:2841:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAGAACTA ACAGATATAT GT >HWI-ST960:105:D10GVACXX:2:1101:3211:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGTAAT GTAGTCTTTA AA >HWI-ST960:105:D10GVACXX:2:1101:3145:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGGCTGTG GAGTAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:3082:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTGTGTT GGCGTTTTAT CT >HWI-ST960:105:D10GVACXX:2:1101:3160:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTTGTTG GCCAAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:3135:2214 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCGACAGGAG AGGTGATCGG AGT >HWI-ST960:105:D10GVACXX:2:1101:3213:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGTTCTGT TGAAGGAGCT TTT >HWI-ST960:105:D10GVACXX:2:1101:3036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATATAC TTCACAACTC TG >HWI-ST960:105:D10GVACXX:2:1101:3140:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGCAAATA AGTCAAAACT TT >HWI-ST960:105:D10GVACXX:2:1101:3106:2228 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTTAGCTCG ACCTAACACT T >HWI-ST960:105:D10GVACXX:2:1101:3085:2237 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTCATCAAC TTTGTCTCTG CTT >HWI-ST960:105:D10GVACXX:2:1101:3151:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATTCCAT GTACTTACAT TCC >HWI-ST960:105:D10GVACXX:2:1101:3041:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGTAATAC CTTTTATATA TAG >HWI-ST960:105:D10GVACXX:2:1101:3218:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGCCCAAA CTGCATGCAC AT >HWI-ST960:105:D10GVACXX:2:1101:3440:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGGATT GAAGGGAGCT C >HWI-ST960:105:D10GVACXX:2:1101:3302:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCAAGTCAT GACTCATGAG CTA >HWI-ST960:105:D10GVACXX:2:1101:3369:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTGTCAT ATTTGCGATG TAT >HWI-ST960:105:D10GVACXX:2:1101:3257:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTAAA CTCTCGTGTG GCT >HWI-ST960:105:D10GVACXX:2:1101:3285:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGAGATGC AAAACAGTAG TTT >HWI-ST960:105:D10GVACXX:2:1101:3316:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAAATC TTAATCTCAA AT >HWI-ST960:105:D10GVACXX:2:1101:3597:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCCCCCG TGAGTTACTT CAC >HWI-ST960:105:D10GVACXX:2:1101:3651:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATATGTA GGCTAAAAAA AAA >HWI-ST960:105:D10GVACXX:2:1101:3568:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATTTATG TTTTGGACTT GT >HWI-ST960:105:D10GVACXX:2:1101:3545:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGTGTGT TGTGGTTTTT AT >HWI-ST960:105:D10GVACXX:2:1101:3669:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTGTGTT GGCGTTTTAT CT >HWI-ST960:105:D10GVACXX:2:1101:3587:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAAGTGT AGAATGCATA CAA >HWI-ST960:105:D10GVACXX:2:1101:3570:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTGTAT GATTGAAGAA AT >HWI-ST960:105:D10GVACXX:2:1101:3530:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTAACGAAA ACTATTTAAA AT >HWI-ST960:105:D10GVACXX:2:1101:3706:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGGCGAG TGTATCTCAA CAA >HWI-ST960:105:D10GVACXX:2:1101:3775:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTACATTA AGGCAGTTCA TTG >HWI-ST960:105:D10GVACXX:2:1101:3902:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCACAAA TGAACTTAAA CT >HWI-ST960:105:D10GVACXX:2:1101:3885:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTACCTACT CGTCGTACAT TTT >HWI-ST960:105:D10GVACXX:2:1101:3807:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATCTCGG ACCAAAGAGA GC >HWI-ST960:105:D10GVACXX:2:1101:3780:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGCATGTT GTGCACCGGC TCC >HWI-ST960:105:D10GVACXX:2:1101:3853:2215 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCTCCGATGA TGATCAAATC AT >HWI-ST960:105:D10GVACXX:2:1101:3946:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAGTCT TTTGGTATTT TA >HWI-ST960:105:D10GVACXX:2:1101:3976:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTGTTCG GCTTTGGATT AAG >HWI-ST960:105:D10GVACXX:2:1101:3866:2227 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATACGAT ATGTATATGT AC >HWI-ST960:105:D10GVACXX:2:1101:3816:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAGGTCT TGTGTAGAAA CT >HWI-ST960:105:D10GVACXX:2:1101:3779:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTTGAGT TTCGAGTTAT CTG >HWI-ST960:105:D10GVACXX:2:1101:3799:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTCTATC TACTACTTTT TC >HWI-ST960:105:D10GVACXX:2:1101:3759:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAACTAGTA TAGTCAGAAA AT >HWI-ST960:105:D10GVACXX:2:1101:3912:2249 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCATGTGAAC AAGAACATAT CCT >HWI-ST960:105:D10GVACXX:2:1101:4099:2173 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTTGGCTCA TGAAGTAAAA TAA >HWI-ST960:105:D10GVACXX:2:1101:4193:2190 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACTTTACA GCTTCTTCTT AT >HWI-ST960:105:D10GVACXX:2:1101:4045:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACTGTGTT GGCGTTTTAT CT >HWI-ST960:105:D10GVACXX:2:1101:4171:2195 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCGAAGTTGA AGAACCTATA A >HWI-ST960:105:D10GVACXX:2:1101:4159:2232 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCGTATCAAA CGTAGAGGCA G >HWI-ST960:105:D10GVACXX:2:1101:4186:2233 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTAGTCA GCTGCAACAC TTT >HWI-ST960:105:D10GVACXX:2:1101:4072:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTAACACCA AACAACTCTT TCT >HWI-ST960:105:D10GVACXX:2:1101:4053:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGGAGG TTTGAGATAT AA >HWI-ST960:105:D10GVACXX:2:1101:4001:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCAAATGA GAACTTTGAA GGC >HWI-ST960:105:D10GVACXX:2:1101:4487:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAGCATGT AGTTTGATGA TC >HWI-ST960:105:D10GVACXX:2:1101:4487:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAATTGTT ACGCAACAAA CT >HWI-ST960:105:D10GVACXX:2:1101:4428:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAAATAT TTTTTCTATT CA >HWI-ST960:105:D10GVACXX:2:1101:4264:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTTAATC TGAGTCTCTG CTT >HWI-ST960:105:D10GVACXX:2:1101:4422:2216 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACTTTACA CGACAAAATA A >HWI-ST960:105:D10GVACXX:2:1101:4332:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTCCGA GTACAACTTT GG >HWI-ST960:105:D10GVACXX:2:1101:4424:2238 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTAATCTTG TGTCGGCAGG TGT >HWI-ST960:105:D10GVACXX:2:1101:4369:2249 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCGATAATGA TGATGAAAGA TG >HWI-ST960:105:D10GVACXX:2:1101:4279:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATGTAG AACTCTTTGC TT >HWI-ST960:105:D10GVACXX:2:1101:4583:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAGTGA AATACACTCT CT >HWI-ST960:105:D10GVACXX:2:1101:4599:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTGTTATC GTGTCTGTAA GC >HWI-ST960:105:D10GVACXX:2:1101:4699:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTGCCTTC AAGTTAACTT TGT >HWI-ST960:105:D10GVACXX:2:1101:4615:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGTCTTCT TCTTCTGTAT TA >HWI-ST960:105:D10GVACXX:2:1101:4505:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATCCTATG CTTTGGTCAT AT >HWI-ST960:105:D10GVACXX:2:1101:4515:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTACTTAG ACTCATGCTT GT >HWI-ST960:105:D10GVACXX:2:1101:4695:2199 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAATGACTG TAACTTACTC TTC >HWI-ST960:105:D10GVACXX:2:1101:4586:2200 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATAGGA ATCTGTAACT TTT >HWI-ST960:105:D10GVACXX:2:1101:4624:2201 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATTTGCG ATGTATCATG TAT >HWI-ST960:105:D10GVACXX:2:1101:4717:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTGGTT TATTTACATG TTT >HWI-ST960:105:D10GVACXX:2:1101:4738:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATAGCTTC TCTGTTATGT CT >HWI-ST960:105:D10GVACXX:2:1101:4745:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTGATAT CTAAGCTTAT GT >HWI-ST960:105:D10GVACXX:2:1101:4619:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTCAGATT TCTTACATTC AA >HWI-ST960:105:D10GVACXX:2:1101:4707:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCAGTGTTT GTCTGAACTC TG >HWI-ST960:105:D10GVACXX:2:1101:4754:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATCGTCGT CAAGCCTGCC AC >HWI-ST960:105:D10GVACXX:2:1101:4768:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAAACTTCT CTGTTTAGTT TGT >HWI-ST960:105:D10GVACXX:2:1101:4842:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAATCAT TATAGAGATG GT >HWI-ST960:105:D10GVACXX:2:1101:4964:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCAAGTCAT GACTCATGAG AT >HWI-ST960:105:D10GVACXX:2:1101:4787:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAACAAACT TGCATGTCGG CAC >HWI-ST960:105:D10GVACXX:2:1101:4867:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCTTCTTT CCAATCTTAT CAC >HWI-ST960:105:D10GVACXX:2:1101:4934:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTAG TAACTGAAAA CG >HWI-ST960:105:D10GVACXX:2:1101:4988:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTCTTTC TCGAGAAATC GG >HWI-ST960:105:D10GVACXX:2:1101:4973:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGCTGTAA TTACAGATTG AA >HWI-ST960:105:D10GVACXX:2:1101:4783:2210 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCGATGAATA CATCATGGTA GTG >HWI-ST960:105:D10GVACXX:2:1101:4861:2212 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATGTTT AGTTTAGAAG AA >HWI-ST960:105:D10GVACXX:2:1101:4929:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACTGTGT CTCATCACTC AA >HWI-ST960:105:D10GVACXX:2:1101:4966:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATATTCAA ACTCTTGGAC TGA >HWI-ST960:105:D10GVACXX:2:1101:4877:2249 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTA TCCTTCCTAC TTGAAGAAGG TTG >HWI-ST960:105:D10GVACXX:2:1101:5029:2168 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTTTTGGTT CTGTAGACAC AC >HWI-ST960:105:D10GVACXX:2:1101:5174:2170 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATATAAT ATTCCCTAAG AA >HWI-ST960:105:D10GVACXX:2:1101:5153:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATACCCC GAAAATTAGA TC >HWI-ST960:105:D10GVACXX:2:1101:5078:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCTTGGTC TGGTGGTAAC AAT >HWI-ST960:105:D10GVACXX:2:1101:5182:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTTGTCA ACTTCAATTT CAG >HWI-ST960:105:D10GVACXX:2:1101:5054:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTACTGTA TCTCATTAGC TGA >HWI-ST960:105:D10GVACXX:2:1101:5208:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATGTTTC TCTTGGAACG AA >HWI-ST960:105:D10GVACXX:2:1101:5105:2206 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATGAACTG TATTAAACTT TT >HWI-ST960:105:D10GVACXX:2:1101:5029:2212 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAACATTTC GAACAATGAA CAA >HWI-ST960:105:D10GVACXX:2:1101:5084:2222 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTACCTCT CTCTGACTTC AC >HWI-ST960:105:D10GVACXX:2:1101:5223:2223 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCCGGAGTTT TTTCAGCAGT TC >HWI-ST960:105:D10GVACXX:2:1101:5173:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATGTGT AATGATTCCT TC >HWI-ST960:105:D10GVACXX:2:1101:5208:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTTACTT TGATCAGAAA TT >HWI-ST960:105:D10GVACXX:2:1101:5101:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAACTCTA CCTTTATTAC AGT >HWI-ST960:105:D10GVACXX:2:1101:5189:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTACAAAA CTTTCTAATT TG >HWI-ST960:105:D10GVACXX:2:1101:5018:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATGTAG AATATGAGTT TA >HWI-ST960:105:D10GVACXX:2:1101:5160:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTGCTTGA TTTTGAAGTT AG >HWI-ST960:105:D10GVACXX:2:1101:5498:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGCGAGAG TTCTTGAACT GA >HWI-ST960:105:D10GVACXX:2:1101:5435:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATAAGGA CTGTGAAGTG TG >HWI-ST960:105:D10GVACXX:2:1101:5472:2190 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCACTGTAA TCTCACGGTG TGT >HWI-ST960:105:D10GVACXX:2:1101:5358:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTAAT GTAGTCTTTA AA >HWI-ST960:105:D10GVACXX:2:1101:5420:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCGTTTGAT TTGCAAGCTG >HWI-ST960:105:D10GVACXX:2:1101:5318:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTTGTAG CAAGGCACTG AT >HWI-ST960:105:D10GVACXX:2:1101:5357:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTCATTT CTGCTCTTAT CAC >HWI-ST960:105:D10GVACXX:2:1101:5300:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATGTAGA ACACACATGA TTT >HWI-ST960:105:D10GVACXX:2:1101:5485:2228 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAAATATC GTATCCGTTC AA >HWI-ST960:105:D10GVACXX:2:1101:5295:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCAAAGACT TGGACCTTCT TTC >HWI-ST960:105:D10GVACXX:2:1101:5281:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGGAGCGTA CCGACATGCG GT >HWI-ST960:105:D10GVACXX:2:1101:5679:2172 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTAACAATA TTCTCATGCA CCT >HWI-ST960:105:D10GVACXX:2:1101:5663:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTGTAA TCTGACTCTC TT >HWI-ST960:105:D10GVACXX:2:1101:5539:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTGAAAGA AAGAGCCATT GGT >HWI-ST960:105:D10GVACXX:2:1101:5728:2197 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATCTGTAT AAATAGTTTT AA >HWI-ST960:105:D10GVACXX:2:1101:5500:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTATCAAT TGAACTAGAT TCA >HWI-ST960:105:D10GVACXX:2:1101:5592:2204 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCAATAAAGC TGTTGAATGA GAT >HWI-ST960:105:D10GVACXX:2:1101:5553:2233 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCGATCTGTA AACTAAAAAA AC >HWI-ST960:105:D10GVACXX:2:1101:5604:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTTGATT ACCATAGCAT TT >HWI-ST960:105:D10GVACXX:2:1101:5743:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGGTTTT AAGTTCTTAG AAC >HWI-ST960:105:D10GVACXX:2:1101:5682:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTTGAGT ATGTAGAATC TG >HWI-ST960:105:D10GVACXX:2:1101:5979:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTCTCTAG AAAATATCAG A >HWI-ST960:105:D10GVACXX:2:1101:5958:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGCGATGA TGATAAAATA GC >HWI-ST960:105:D10GVACXX:2:1101:5985:2215 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATAGTT TTGTTGTTTC TT >HWI-ST960:105:D10GVACXX:2:1101:5952:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTAGCAGTA CAATTGCAGA AGT >HWI-ST960:105:D10GVACXX:2:1101:5970:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTTATGTA GTCTCATTTC CT >HWI-ST960:105:D10GVACXX:2:1101:5909:2233 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCACCAGTTT TACAGAGTGT TT >HWI-ST960:105:D10GVACXX:2:1101:5792:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATATAC TTCACAACTC TG >HWI-ST960:105:D10GVACXX:2:1101:5990:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACGGGAAG GTGATATTTG CT >HWI-ST960:105:D10GVACXX:2:1101:6014:2179 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTACTTCT AAGTTTAGTA AC >HWI-ST960:105:D10GVACXX:2:1101:6138:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTTATAT GAACCAATAA TAG >HWI-ST960:105:D10GVACXX:2:1101:6181:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCACAAA ATATATAGGA AGT >HWI-ST960:105:D10GVACXX:2:1101:6001:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTGTGAA TCTGATTATA CAC >HWI-ST960:105:D10GVACXX:2:1101:6161:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAAGTCA TAATAATAGT AGC >HWI-ST960:105:D10GVACXX:2:1101:6053:2206 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTTGTTG GCATGAGAAC CAA >HWI-ST960:105:D10GVACXX:2:1101:6128:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATTGTTG TACTCTTTAA TAT >HWI-ST960:105:D10GVACXX:2:1101:6082:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTTTGTG TGAAAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:6229:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTTGGTG AAGTTTTTAA GT >HWI-ST960:105:D10GVACXX:2:1101:6024:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAAACCT ATAATATTTC TT >HWI-ST960:105:D10GVACXX:2:1101:6181:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCGGCTAA TACCTAATGT CA >HWI-ST960:105:D10GVACXX:2:1101:6060:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGAATCA TGTTGCTTTA CT >HWI-ST960:105:D10GVACXX:2:1101:6084:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATGTGTT CTCTCTGTTC AA >HWI-ST960:105:D10GVACXX:2:1101:6492:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTCACAT TATGAATATC AA >HWI-ST960:105:D10GVACXX:2:1101:6252:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATATAC TTCACAACTC TG >HWI-ST960:105:D10GVACXX:2:1101:6273:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATGTTGT CTCTCCCTCT TAT >HWI-ST960:105:D10GVACXX:2:1101:6457:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGTGAAAC TCTATCAATT CA >HWI-ST960:105:D10GVACXX:2:1101:6377:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGAATATGT TGCTGTAGTC AC >HWI-ST960:105:D10GVACXX:2:1101:6427:2203 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCAAACCAGA GACAAATGAC AC >HWI-ST960:105:D10GVACXX:2:1101:6279:2218 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTA TCTTGGACTG TGAAGTTTGG CT >HWI-ST960:105:D10GVACXX:2:1101:6366:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGATGTCG GCGTTGAATA AA >HWI-ST960:105:D10GVACXX:2:1101:6393:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATTGCAG TAGAACATAA GT >HWI-ST960:105:D10GVACXX:2:1101:6268:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAACTCTTG TGTACCATAA AAA >HWI-ST960:105:D10GVACXX:2:1101:6467:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATCACCA TGTTCCAATT TC >HWI-ST960:105:D10GVACXX:2:1101:6481:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATACTAG TGTTTAAGAA GTT >HWI-ST960:105:D10GVACXX:2:1101:6397:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTAACTTT GGCGAATGGA TAC >HWI-ST960:105:D10GVACXX:2:1101:6429:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTATATAT GGAGAAAATG GA >HWI-ST960:105:D10GVACXX:2:1101:6525:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTGTAAG CTGAGGAACT CT >HWI-ST960:105:D10GVACXX:2:1101:6517:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATGGCAC GGCTATGAAA TCT >HWI-ST960:105:D10GVACXX:2:1101:6700:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACATCTCA CTGCTCACTA CTC >HWI-ST960:105:D10GVACXX:2:1101:6538:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGCTAGAG AGAGGAGGAG AC >HWI-ST960:105:D10GVACXX:2:1101:6575:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTTTAA CACCTCTACT TTT >HWI-ST960:105:D10GVACXX:2:1101:6501:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTTTATGG CTCTAGTACA AGC >HWI-ST960:105:D10GVACXX:2:1101:6631:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTATCTCT AAAATTGCAA AT >HWI-ST960:105:D10GVACXX:2:1101:6672:2205 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCATGGTTGC TTTAATATTT TT >HWI-ST960:105:D10GVACXX:2:1101:6579:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCGACTTTG ATCCAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:6552:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCATCTTTAG CTTTATTTAC TC >HWI-ST960:105:D10GVACXX:2:1101:6685:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATTATTA TCAATAGCTC TTC >HWI-ST960:105:D10GVACXX:2:1101:6503:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTAGGGG CTGATTTGTC TT >HWI-ST960:105:D10GVACXX:2:1101:6613:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCTACCAT TATGCACTAT TT >HWI-ST960:105:D10GVACXX:2:1101:6670:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCGGCGTGA AAGGGCGACT AAA >HWI-ST960:105:D10GVACXX:2:1101:6721:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAAACTT TCTTAGCTTG TCC >HWI-ST960:105:D10GVACXX:2:1101:6642:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGGGTGATG AACGAAATAA AAA >HWI-ST960:105:D10GVACXX:2:1101:6589:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTAAAGA CAGAGAGATA GA >HWI-ST960:105:D10GVACXX:2:1101:6684:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGATCGAAA CCAAACACCG AT >HWI-ST960:105:D10GVACXX:2:1101:6830:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTGTCAT TCTCTAAATA AC >HWI-ST960:105:D10GVACXX:2:1101:6954:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATAACT CTCTCGCCTT TGT >HWI-ST960:105:D10GVACXX:2:1101:6754:2179 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAAGTCG TATCTAGGTG TGT >HWI-ST960:105:D10GVACXX:2:1101:6877:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACAAAGT CGTTGTAGTA TAC >HWI-ST960:105:D10GVACXX:2:1101:6970:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATCACACT GTCAAATCCG AA >HWI-ST960:105:D10GVACXX:2:1101:6918:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTCGGCT CTGTTCATAT AC >HWI-ST960:105:D10GVACXX:2:1101:6851:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTTCTGG CTGTAGAATC TT >HWI-ST960:105:D10GVACXX:2:1101:6836:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCACGCACA CCGCGTGTAG AG >HWI-ST960:105:D10GVACXX:2:1101:6948:2228 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCCGATAGAG AACCTTGCTG ACC >HWI-ST960:105:D10GVACXX:2:1101:6923:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATTTTA TGTGGTGTTA CTT >HWI-ST960:105:D10GVACXX:2:1101:6971:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATCAGTGA TGAAATTATG TC >HWI-ST960:105:D10GVACXX:2:1101:6883:2236 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGAGTGAG ATATAAAATG GG >HWI-ST960:105:D10GVACXX:2:1101:6822:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGAATTCAG ACTGTGAAAC TGC >HWI-ST960:105:D10GVACXX:2:1101:7018:2176 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCGGAGTTTT TTCAGCAGTT CT >HWI-ST960:105:D10GVACXX:2:1101:7182:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTGTATT TGTGCGTGTA GC >HWI-ST960:105:D10GVACXX:2:1101:7145:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATAATAAG ACTCTTAATC AA >HWI-ST960:105:D10GVACXX:2:1101:7091:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGTAAT GTAGTCTTAA AA >HWI-ST960:105:D10GVACXX:2:1101:7123:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTCCTTGA CTGGAAAAAT GT >HWI-ST960:105:D10GVACXX:2:1101:7068:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATGTA CCGATGCATA GT >HWI-ST960:105:D10GVACXX:2:1101:7245:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTTACC ATGGAACGAA CAT >HWI-ST960:105:D10GVACXX:2:1101:7109:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTGTAAT TCAGTTAGCT CAA >HWI-ST960:105:D10GVACXX:2:1101:7209:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTGTCAA TGCATAGACA AAA >HWI-ST960:105:D10GVACXX:2:1101:7060:2201 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGTGTGT TGGTGGATAT AAC >HWI-ST960:105:D10GVACXX:2:1101:7155:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTGTTGG CCTTTAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:7198:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATATAT TTCGTTTCAT TT >HWI-ST960:105:D10GVACXX:2:1101:7115:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAAGGCT GTGGAGGTTA TC >HWI-ST960:105:D10GVACXX:2:1101:7149:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTTGTTA GACTCTTCGA TTT >HWI-ST960:105:D10GVACXX:2:1101:7127:2244 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTAGA TACTGATATT A >HWI-ST960:105:D10GVACXX:2:1101:7018:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTTATAT GAACCAATAA TAG >HWI-ST960:105:D10GVACXX:2:1101:7382:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTAGTAGAC TTGCAAAGAT CGT >HWI-ST960:105:D10GVACXX:2:1101:7449:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATACCCC GAAAATTAGA TC >HWI-ST960:105:D10GVACXX:2:1101:7359:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGGCTGAT TGTAGAATGG TT >HWI-ST960:105:D10GVACXX:2:1101:7292:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTCAA TCCATGGTTT TCTCAAAGTT TTC >HWI-ST960:105:D10GVACXX:2:1101:7393:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTCT CTGTACTGTA AC >HWI-ST960:105:D10GVACXX:2:1101:7359:2210 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGA TCAGAGATCG GAAGAGATGG CTT >HWI-ST960:105:D10GVACXX:2:1101:7415:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTAATTA TTCGTATGAA CT >HWI-ST960:105:D10GVACXX:2:1101:7403:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCGTCTTAC CATTTCTTTC AT >HWI-ST960:105:D10GVACXX:2:1101:7373:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGTCTG TCTAGTCTAT TG >HWI-ST960:105:D10GVACXX:2:1101:7324:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATCAAAT GTATTATATA TAT >HWI-ST960:105:D10GVACXX:2:1101:7309:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTGAGTTT TTACATGTTT GT >HWI-ST960:105:D10GVACXX:2:1101:7475:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTGACTG TATTGAGCAA CC >HWI-ST960:105:D10GVACXX:2:1101:7649:2170 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTGAGTAGA CAATTTAATC A >HWI-ST960:105:D10GVACXX:2:1101:7708:2170 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGTTTAAT AAAACAGAAC AA >HWI-ST960:105:D10GVACXX:2:1101:7709:2191 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCTCTCTC TTACCTTTCT CT >HWI-ST960:105:D10GVACXX:2:1101:7690:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTCGATT AGTACCGTTA GTG >HWI-ST960:105:D10GVACXX:2:1101:7607:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCCGGAATG GTGCCTTTGT TAC >HWI-ST960:105:D10GVACXX:2:1101:7698:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTCTGGCT TTGCTCAGAT TT >HWI-ST960:105:D10GVACXX:2:1101:7518:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAATTCTTT TACCGGGTTG AG >HWI-ST960:105:D10GVACXX:2:1101:7534:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATAATGAA TGTTTCGGAC TTC >HWI-ST960:105:D10GVACXX:2:1101:7679:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCGGTGA GTGGAACTTC TT >HWI-ST960:105:D10GVACXX:2:1101:7747:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCACGAGTC GAGGCTCTCA ATA >HWI-ST960:105:D10GVACXX:2:1101:7610:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCAGTGGT AGAGCGCGTG GC >HWI-ST960:105:D10GVACXX:2:1101:7532:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATGTTC ACTGTTCTCT GC >HWI-ST960:105:D10GVACXX:2:1101:7676:2238 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCCAGCCGTC GGATACTGAC TT >HWI-ST960:105:D10GVACXX:2:1101:7641:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATCTGTAG CCTCTCTTTT AGT >HWI-ST960:105:D10GVACXX:2:1101:7966:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGCAACT GCAAATTCTG CA >HWI-ST960:105:D10GVACXX:2:1101:7948:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTGCTGT GGATGATCTG GT >HWI-ST960:105:D10GVACXX:2:1101:7864:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCGGAAGAAC TCTGGAAGTG AA >HWI-ST960:105:D10GVACXX:2:1101:7912:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACAAGAT GTTTAATCAT CC >HWI-ST960:105:D10GVACXX:2:1101:7970:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACAATTGT TGTCTTGTAG TA >HWI-ST960:105:D10GVACXX:2:1101:7819:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAATTGT TTCTTAGCAT CT >HWI-ST960:105:D10GVACXX:2:1101:7762:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTACTTTAT AAGGACTGTG AA >HWI-ST960:105:D10GVACXX:2:1101:7847:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGCAACC CTGTCTTGCT TTA >HWI-ST960:105:D10GVACXX:2:1101:7775:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTATTGTG TTACTGAATC TT >HWI-ST960:105:D10GVACXX:2:1101:7900:2219 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTACGCC CGAACGCAAA CC >HWI-ST960:105:D10GVACXX:2:1101:7800:2227 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTCTTATGA TGTCAAAACT TTC >HWI-ST960:105:D10GVACXX:2:1101:7973:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTATGTGT TCTGCAGATC GA >HWI-ST960:105:D10GVACXX:2:1101:7844:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTCGTTG GGTTTTCTTC AT >HWI-ST960:105:D10GVACXX:2:1101:7863:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATAAATTT TCGAAGGAGA CAA >HWI-ST960:105:D10GVACXX:2:1101:7912:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCGTGTGTAA CCTCATATGG AC >HWI-ST960:105:D10GVACXX:2:1101:7940:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCGTGTCAA GTGTAGAATC AA >HWI-ST960:105:D10GVACXX:2:1101:8023:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGTATCT TGTTGTTTAT CTA >HWI-ST960:105:D10GVACXX:2:1101:8157:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCAGTGGT AGAGCGCGTG GC >HWI-ST960:105:D10GVACXX:2:1101:8117:2186 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCACTGAATC GACTTTGGGC AAA >HWI-ST960:105:D10GVACXX:2:1101:8197:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATGGTGCT TAAAAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:8236:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTCG GCTTAAACTC TAT >HWI-ST960:105:D10GVACXX:2:1101:8088:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGGAAA TGTGCTATGG AC >HWI-ST960:105:D10GVACXX:2:1101:8085:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCGCAGTC GCTAAGCGTC AC >HWI-ST960:105:D10GVACXX:2:1101:8003:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATATTTGT GGATGATGAA GA >HWI-ST960:105:D10GVACXX:2:1101:8138:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTATATGA TTCTACTTAG TCA >HWI-ST960:105:D10GVACXX:2:1101:8069:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGGTACTA TGAACATTGT GAC >HWI-ST960:105:D10GVACXX:2:1101:8355:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATGTGT AACCCTGTCC TT >HWI-ST960:105:D10GVACXX:2:1101:8375:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TATTGCTATA GAGTCACGCA TCT >HWI-ST960:105:D10GVACXX:2:1101:8257:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACCTGGAG ACTCATGTGT TGA >HWI-ST960:105:D10GVACXX:2:1101:8438:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTGGTTT GGATTTTGGT TA >HWI-ST960:105:D10GVACXX:2:1101:8299:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCTCTGG CTGTTGAATA GA >HWI-ST960:105:D10GVACXX:2:1101:8333:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGCTTGCA AGTTCTCTCT GAA >HWI-ST960:105:D10GVACXX:2:1101:8309:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACTGTGTT GGCGTTTTAT CTG >HWI-ST960:105:D10GVACXX:2:1101:8363:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCAAGCATG ATGAATTGAT GAG >HWI-ST960:105:D10GVACXX:2:1101:8494:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTTGCAT TGATTGTGGT TAC >HWI-ST960:105:D10GVACXX:2:1101:8291:2212 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTCTACTCT ACTAAACCTC TGT >HWI-ST960:105:D10GVACXX:2:1101:8482:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATCTTCCG TCTGTTTCTG AT >HWI-ST960:105:D10GVACXX:2:1101:8322:2218 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTTGACCGA TGCTCGGACA A >HWI-ST960:105:D10GVACXX:2:1101:8388:2225 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCGTGTGTAT TTAGTAATTC AT >HWI-ST960:105:D10GVACXX:2:1101:8442:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTTTCTA TGTTGTTTGG TAG >HWI-ST960:105:D10GVACXX:2:1101:8339:2233 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTA TCATCTCTAG AACTCTTTAT AAT >HWI-ST960:105:D10GVACXX:2:1101:8376:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGTGTCA GATTCTAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:8457:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTCTGTG GATTATGCTT TA >HWI-ST960:105:D10GVACXX:2:1101:8627:2171 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGGTAAAT TTGTCTGAAT TA >HWI-ST960:105:D10GVACXX:2:1101:8743:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCATCTT TTCTTATGTA AA >HWI-ST960:105:D10GVACXX:2:1101:8722:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTAG AGAAAGTGAT TA >HWI-ST960:105:D10GVACXX:2:1101:8678:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGATGTAT ATTTACGAGA TGT >HWI-ST960:105:D10GVACXX:2:1101:8565:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGTCCTTC GGATCACTCA ATT >HWI-ST960:105:D10GVACXX:2:1101:8583:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAACGCT TTTATGTGCT TCT >HWI-ST960:105:D10GVACXX:2:1101:8633:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATACATA TTGGGTTGTG ATT >HWI-ST960:105:D10GVACXX:2:1101:8687:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTTCTGT AGACTATGTG TTG >HWI-ST960:105:D10GVACXX:2:1101:8605:2201 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTTTCTTGT CTAGTCGGTT TAT >HWI-ST960:105:D10GVACXX:2:1101:8532:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATGAATG TGTAGAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:8688:2216 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTGGGGAA GGATCAGATG CA >HWI-ST960:105:D10GVACXX:2:1101:8560:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATTGGTG CCTGTAGGTC AG >HWI-ST960:105:D10GVACXX:2:1101:8658:2230 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTGCTATA GAATCTGGAC AAA >HWI-ST960:105:D10GVACXX:2:1101:8538:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTTATCT TTTACTTTCC TC >HWI-ST960:105:D10GVACXX:2:1101:8669:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTACTGTT TTTTCCGCCT TC >HWI-ST960:105:D10GVACXX:2:1101:8917:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATGTTGTT GTTGCATGCT GTG >HWI-ST960:105:D10GVACXX:2:1101:8755:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATGATGTC GTTGGGTCTT TGT >HWI-ST960:105:D10GVACXX:2:1101:8885:2196 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTCCGATGA TGATCAAATC AT >HWI-ST960:105:D10GVACXX:2:1101:8967:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTCTTT ATTCCTGGGT TGT >HWI-ST960:105:D10GVACXX:2:1101:8797:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTAACTC TTGCCTCTTC TT >HWI-ST960:105:D10GVACXX:2:1101:8831:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTTGGGT TTGTGGTGGG GGT >HWI-ST960:105:D10GVACXX:2:1101:8957:2220 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTCTTTA GCATCGACTG TT >HWI-ST960:105:D10GVACXX:2:1101:8751:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTGTTTG TGTTTAAGTG CT >HWI-ST960:105:D10GVACXX:2:1101:8914:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCGTTTTGG CTTTCGTTCT GT >HWI-ST960:105:D10GVACXX:2:1101:8937:2229 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTGGAATGA TGATAACGAT TTT >HWI-ST960:105:D10GVACXX:2:1101:8832:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTGTCAG TCTAAGAAAA TG >HWI-ST960:105:D10GVACXX:2:1101:8894:2244 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCGAATGTTT AAATTGGATC AA >HWI-ST960:105:D10GVACXX:2:1101:8849:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTACTGT AGTATATATG AT >HWI-ST960:105:D10GVACXX:2:1101:9130:2168 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGGAATTG TTGAGTTTGG TA >HWI-ST960:105:D10GVACXX:2:1101:9203:2174 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTTGACTGT GATTTAAACG AG >HWI-ST960:105:D10GVACXX:2:1101:9183:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTACTCTA TCTTAAACAT GT >HWI-ST960:105:D10GVACXX:2:1101:9125:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATCGGAT TGTCAAATGT CT >HWI-ST960:105:D10GVACXX:2:1101:9001:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTCTTGT TGTCTAACTC TC >HWI-ST960:105:D10GVACXX:2:1101:9175:2204 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGA TCTGAGAATA AGAACATACA TAA >HWI-ST960:105:D10GVACXX:2:1101:9224:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATCGTAAA AACTTTGGGA TGC >HWI-ST960:105:D10GVACXX:2:1101:9118:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATAGTTC AGTCGACATG AAT >HWI-ST960:105:D10GVACXX:2:1101:9087:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATATGGAT GGATAATTTT CT >HWI-ST960:105:D10GVACXX:2:1101:9013:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGGAGCCT CTGTAATTTT GT >HWI-ST960:105:D10GVACXX:2:1101:9153:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTCTTCGA ATGACGAGTT CC >HWI-ST960:105:D10GVACXX:2:1101:9188:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCCTTTGTCG CTAAGATTCG A >HWI-ST960:105:D10GVACXX:2:1101:9022:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAAAATA AACACATGTA CTT >HWI-ST960:105:D10GVACXX:2:1101:9098:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCGAGGAGAG CAGTCTATTC TG >HWI-ST960:105:D10GVACXX:2:1101:9115:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTGTTTAG TTGGCGGTTT CAC >HWI-ST960:105:D10GVACXX:2:1101:9136:2239 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTTGCTT CCTTTAACAA AA >HWI-ST960:105:D10GVACXX:2:1101:9477:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTTATGG CACAACATGT AA >HWI-ST960:105:D10GVACXX:2:1101:9421:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCCCAGCCT CATAGAGGAA CTG >HWI-ST960:105:D10GVACXX:2:1101:9299:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACCAAACT TTTCAAACCA TGT >HWI-ST960:105:D10GVACXX:2:1101:9456:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATTTCGG AAATGCTAAT CG >HWI-ST960:105:D10GVACXX:2:1101:9347:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGCATAATA ATGTATTTAT TTG >HWI-ST960:105:D10GVACXX:2:1101:9436:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTATGAG TGTGCGTCTC AC >HWI-ST960:105:D10GVACXX:2:1101:9384:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTCTGTTA CACGCCGAGA TC >HWI-ST960:105:D10GVACXX:2:1101:9328:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACTGTTGC AGTCGGTGTT AT >HWI-ST960:105:D10GVACXX:2:1101:9477:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTGT GCTGCTTTCT CT >HWI-ST960:105:D10GVACXX:2:1101:9563:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCCTCGACA CTGTTACTCC AC >HWI-ST960:105:D10GVACXX:2:1101:9614:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTGTCAT ATTTGCGATG TAT >HWI-ST960:105:D10GVACXX:2:1101:9676:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTAAAT CATTGTCTGA ATT >HWI-ST960:105:D10GVACXX:2:1101:9526:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATCTTTT GTATTTTGCT GT >HWI-ST960:105:D10GVACXX:2:1101:9622:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTGTACCT GTTATGCTTT AAA >HWI-ST960:105:D10GVACXX:2:1101:9597:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGTAGCTG TGGAATGAAA GT >HWI-ST960:105:D10GVACXX:2:1101:9507:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCTAGAG CTCTGATGAG TT >HWI-ST960:105:D10GVACXX:2:1101:9613:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTTTTCAT AACTCATCCT ACT >HWI-ST960:105:D10GVACXX:2:1101:9741:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATGAGAC TGTATCCTTT AT >HWI-ST960:105:D10GVACXX:2:1101:9572:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATTAAA ATTAGAACAA AT >HWI-ST960:105:D10GVACXX:2:1101:9606:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTACATATA GTAGTGGAGG CCT >HWI-ST960:105:D10GVACXX:2:1101:9995:2170 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGGGAA CTCTTTTGGA CC >HWI-ST960:105:D10GVACXX:2:1101:9998:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCTTATT AGTTTTAACT TC >HWI-ST960:105:D10GVACXX:2:1101:9771:2192 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCCCTATAAA TAAAAAACAG AC >HWI-ST960:105:D10GVACXX:2:1101:9841:2194 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGA TCTACACCAA ACTCTGGTAC AGT >HWI-ST960:105:D10GVACXX:2:1101:9751:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATTGTTG TAGGCTGTGG TCC >HWI-ST960:105:D10GVACXX:2:1101:9885:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTTTG TGTAACTGTA AC >HWI-ST960:105:D10GVACXX:2:1101:9758:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTGGCGA CTTTCTACCG CAC >HWI-ST960:105:D10GVACXX:2:1101:9838:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTGTAGCT CCATGAACAA AT >HWI-ST960:105:D10GVACXX:2:1101:9815:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAATAAA CACAAAAGTT TT >HWI-ST960:105:D10GVACXX:2:1101:9945:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCAGGATTG GTTTGGTGGA TTA >HWI-ST960:105:D10GVACXX:2:1101:9878:2215 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGAAGCC AGATCAGAAT CTT >HWI-ST960:105:D10GVACXX:2:1101:9912:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCAAAGTTA ATTTCTGTTT CT >HWI-ST960:105:D10GVACXX:2:1101:9753:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTACCAA ATAAGCTTAA GTC >HWI-ST960:105:D10GVACXX:2:1101:9999:2231 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTTTGTGAT ATCTGAAAAA CAT >HWI-ST960:105:D10GVACXX:2:1101:9840:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGATTTT TCCTTTGTTA TC >HWI-ST960:105:D10GVACXX:2:1101:9928:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGCAAAGG CAAGGCTCTG CTG >HWI-ST960:105:D10GVACXX:2:1101:9937:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGTCGGCT TAACTAAGGT GGA >HWI-ST960:105:D10GVACXX:2:1101:9908:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAAGAACTC TGTAATTTCT GT >HWI-ST960:105:D10GVACXX:2:1101:10129:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTGTCCT TAATTCATTT AT >HWI-ST960:105:D10GVACXX:2:1101:10012:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTTGTAT CCTTTCTCAT TTA >HWI-ST960:105:D10GVACXX:2:1101:10236:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATATCACC ATGTTCCAAT TTC >HWI-ST960:105:D10GVACXX:2:1101:10124:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGTGTTGG CATGGGCCTC GA >HWI-ST960:105:D10GVACXX:2:1101:10018:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCGGTTGA CTGGAATTAT TTT >HWI-ST960:105:D10GVACXX:2:1101:10188:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGTGAT TGTTGGCAAT AT >HWI-ST960:105:D10GVACXX:2:1101:10113:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAAGTGT AGAATGCATA C >HWI-ST960:105:D10GVACXX:2:1101:10363:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGGATTCT TCGTTCAGGC CAT >HWI-ST960:105:D10GVACXX:2:1101:10329:2196 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCAAGACTGC AACAACTTCT GC >HWI-ST960:105:D10GVACXX:2:1101:10309:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTTCTGT CATCTACATA TGC >HWI-ST960:105:D10GVACXX:2:1101:10373:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGTACTGT ATTTGCTATT CCC >HWI-ST960:105:D10GVACXX:2:1101:10440:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTTTCTT TTTGTCGGCA TC >HWI-ST960:105:D10GVACXX:2:1101:10352:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATTATCT CTGTTGATTG AT >HWI-ST960:105:D10GVACXX:2:1101:10470:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCCTAGAAC TTGCTCAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:10322:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACTGGAAC TCTTTCTTCT AA >HWI-ST960:105:D10GVACXX:2:1101:10300:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGAATCCAT AGTCTTACCA TGA >HWI-ST960:105:D10GVACXX:2:1101:10348:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGACA AGTCGAATCT ATT >HWI-ST960:105:D10GVACXX:2:1101:10434:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTATGTCG TTTCTTTGAA CT >HWI-ST960:105:D10GVACXX:2:1101:10326:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGAGTTG ATTGTGCAAA CAA >HWI-ST960:105:D10GVACXX:2:1101:10707:2172 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATTTAA ATTCCTTCAA GT >HWI-ST960:105:D10GVACXX:2:1101:10553:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATGTGTA GACTTAATTT TTT >HWI-ST960:105:D10GVACXX:2:1101:10597:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATGTA CCGATGCATA GTC >HWI-ST960:105:D10GVACXX:2:1101:10566:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAGTTTT TGGATTGTAA ATT >HWI-ST960:105:D10GVACXX:2:1101:10694:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTAA TGTTAAATAA CTC >HWI-ST960:105:D10GVACXX:2:1101:10746:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTAACAGGG ACAGTCGGGG GGT >HWI-ST960:105:D10GVACXX:2:1101:10522:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTCTGTAC AGATATACTT TTT >HWI-ST960:105:D10GVACXX:2:1101:10609:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTTGGCT TTTCTCTGCT >HWI-ST960:105:D10GVACXX:2:1101:10672:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGGACT CGGATACGCT TCA >HWI-ST960:105:D10GVACXX:2:1101:10584:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGATGTTGA GGCTCAAAAG TT >HWI-ST960:105:D10GVACXX:2:1101:10743:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTCGATAG AACTACAAAG AAT >HWI-ST960:105:D10GVACXX:2:1101:10653:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGTCCTTC GGATCACTCA AT >HWI-ST960:105:D10GVACXX:2:1101:10642:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGATTTTA AAGTGTTACA AG >HWI-ST960:105:D10GVACXX:2:1101:10627:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACAAGTT GGTCTGGGTT GT >HWI-ST960:105:D10GVACXX:2:1101:10734:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAATCTG GGATGAACTC AC >HWI-ST960:105:D10GVACXX:2:1101:10579:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATCTTTA GTAGAACAAA ATC >HWI-ST960:105:D10GVACXX:2:1101:10596:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGGTACTAA TGGCGAAAGA AC >HWI-ST960:105:D10GVACXX:2:1101:10984:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTACGAT GTCTCTGTAC TC >HWI-ST960:105:D10GVACXX:2:1101:10870:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATGGGTTC GACGTTAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:10979:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACTGAAA TGAACCAAAA CC >HWI-ST960:105:D10GVACXX:2:1101:10780:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGGTGG AACTACATTA TC >HWI-ST960:105:D10GVACXX:2:1101:10858:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTTGCG GATTATGCGT TTT >HWI-ST960:105:D10GVACXX:2:1101:10924:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACAAAGT CGTTGTAGTA TAG >HWI-ST960:105:D10GVACXX:2:1101:10881:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCATACTGT GTCTGCTTCT AT >HWI-ST960:105:D10GVACXX:2:1101:10798:2212 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTA TCAATGTAGG TTGTTTTTGG AC >HWI-ST960:105:D10GVACXX:2:1101:10962:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATAGGA ATCTGTAACT TT >HWI-ST960:105:D10GVACXX:2:1101:10898:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATTTC GGCTGTAGCA TGT >HWI-ST960:105:D10GVACXX:2:1101:10771:2225 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGA TCGAGAATGA TGAACCAATT AG >HWI-ST960:105:D10GVACXX:2:1101:10861:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTTA GACTCTTCGA TTT >HWI-ST960:105:D10GVACXX:2:1101:10883:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAATGTTC TCTTTCTGAT TT >HWI-ST960:105:D10GVACXX:2:1101:10793:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAACTAATG GATGTATGAA TAT >HWI-ST960:105:D10GVACXX:2:1101:10996:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTTGTGT TGTTGACTCT GT >HWI-ST960:105:D10GVACXX:2:1101:10908:2243 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTA TCTGGAATGA TGATAACGAT TTT >HWI-ST960:105:D10GVACXX:2:1101:10822:2244 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTGTGTC TCAGAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:11150:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTAG TAACTGAAAA CGG >HWI-ST960:105:D10GVACXX:2:1101:11176:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCTGTTGA CCAAAAAAAA A >HWI-ST960:105:D10GVACXX:2:1101:11080:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTCCATAA GCTTTGATCA CT >HWI-ST960:105:D10GVACXX:2:1101:11039:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTAGTTAGT TGTTTTAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:11213:2190 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAATAAGAA TAAGAATAAG A >HWI-ST960:105:D10GVACXX:2:1101:11039:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGAGAAAA TGAGCATTAT TAT >HWI-ST960:105:D10GVACXX:2:1101:11145:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTTGT CTCTTAATCG GC >HWI-ST960:105:D10GVACXX:2:1101:11168:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATCAATG CTGGTGCTAA CTT >HWI-ST960:105:D10GVACXX:2:1101:11088:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAAGAACAA GAACACATTT AC >HWI-ST960:105:D10GVACXX:2:1101:11184:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACATCCTT TCAAAACAAG TTC >HWI-ST960:105:D10GVACXX:2:1101:11073:2233 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAAGTCT GGAATAGCTT TT >HWI-ST960:105:D10GVACXX:2:1101:11102:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTTGTCG AACTTGTAAA AAA >HWI-ST960:105:D10GVACXX:2:1101:11129:2239 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGGTTGGTT ATACACCAAA CTC >HWI-ST960:105:D10GVACXX:2:1101:11163:2245 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAATAT GTCTGGCTTG TTT >HWI-ST960:105:D10GVACXX:2:1101:11321:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAATCTGT TTGGTTGTGG AA >HWI-ST960:105:D10GVACXX:2:1101:11427:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTCTTGG TAAAGGTTGA GT >HWI-ST960:105:D10GVACXX:2:1101:11305:2204 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTA TCTACTGACC CCGAGGCTTT CGC >HWI-ST960:105:D10GVACXX:2:1101:11259:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATATGTT TCGTAGAACT AT >HWI-ST960:105:D10GVACXX:2:1101:11401:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGTAGAAA ATGAACTATA AAT >HWI-ST960:105:D10GVACXX:2:1101:11352:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTGAATA GTCGGGGTTA CTT >HWI-ST960:105:D10GVACXX:2:1101:11437:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTGCGTC GTATGAGTAA AAG >HWI-ST960:105:D10GVACXX:2:1101:11258:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAACCGAGT ACTTTTGGTA GC >HWI-ST960:105:D10GVACXX:2:1101:11443:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGTAGT GTAGTGGTAA AA >HWI-ST960:105:D10GVACXX:2:1101:11272:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGTGCTTC AACGGCTCTG GT >HWI-ST960:105:D10GVACXX:2:1101:11399:2247 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCATATGAAC TACGTGTGGC TT >HWI-ST960:105:D10GVACXX:2:1101:11611:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGGAGCTC AAGAACGGAA GAT >HWI-ST960:105:D10GVACXX:2:1101:11736:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGAATACTG TGGTTGTTTT AG >HWI-ST960:105:D10GVACXX:2:1101:11736:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGATACAA TTTCGGTTTC GT >HWI-ST960:105:D10GVACXX:2:1101:11623:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTGTTTTG GGGTTTTAAA CAT >HWI-ST960:105:D10GVACXX:2:1101:11724:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTAGGAC AGTTCATGTT TTT >HWI-ST960:105:D10GVACXX:2:1101:11676:2225 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGCATCAA GCTGTAACCG AAC >HWI-ST960:105:D10GVACXX:2:1101:11707:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGGTATGAA CTATGAACAC AA >HWI-ST960:105:D10GVACXX:2:1101:11640:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTTA GACTCTTCGA TTT >HWI-ST960:105:D10GVACXX:2:1101:11532:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACTAGTAA TAGAGCTTGG AA >HWI-ST960:105:D10GVACXX:2:1101:11511:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTGGAGA TATTGGTTAA CT >HWI-ST960:105:D10GVACXX:2:1101:11573:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAACAATTC GGCTAGAAAT TT >HWI-ST960:105:D10GVACXX:2:1101:11773:2169 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTTTCTTAC TTCGGCCTGT T >HWI-ST960:105:D10GVACXX:2:1101:11943:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGATCAT ATGGACGTAA CAT >HWI-ST960:105:D10GVACXX:2:1101:11759:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTGAGCT CTTCTTTTCT TA >HWI-ST960:105:D10GVACXX:2:1101:11857:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCTGTAG TAGGCTTGCA TGC >HWI-ST960:105:D10GVACXX:2:1101:11838:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATCAATG TATTGTATCC G >HWI-ST960:105:D10GVACXX:2:1101:11790:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGAATTTC TGTAGACTAT GT >HWI-ST960:105:D10GVACXX:2:1101:11770:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGGATGCGA TCATACCAGC AC >HWI-ST960:105:D10GVACXX:2:1101:11869:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTGATGTT GGTTTGTAAT AT >HWI-ST960:105:D10GVACXX:2:1101:11959:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTACTGTA CACACAAACT TC >HWI-ST960:105:D10GVACXX:2:1101:11892:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATAAAAT GACTCTGAAA AA >HWI-ST960:105:D10GVACXX:2:1101:11899:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATAATGT AATAGTACTC ACC >HWI-ST960:105:D10GVACXX:2:1101:12088:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTTTGTA CAAATCCAAA CCT >HWI-ST960:105:D10GVACXX:2:1101:12143:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTCTGTC AACCTCTTCG GA >HWI-ST960:105:D10GVACXX:2:1101:12198:2193 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAGGGATGA TGATTCAATT A >HWI-ST960:105:D10GVACXX:2:1101:12019:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATTGTTG AACTTAGAAT CAA >HWI-ST960:105:D10GVACXX:2:1101:12174:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTCTGTAG CTCTAGACCA TTC >HWI-ST960:105:D10GVACXX:2:1101:12126:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATTCCCG TTGAGAGGAT CAT >HWI-ST960:105:D10GVACXX:2:1101:12157:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGCTACTC TCCTCGTCTC CT >HWI-ST960:105:D10GVACXX:2:1101:12048:2210 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTACCACTC TTGCATTTGC AT >HWI-ST960:105:D10GVACXX:2:1101:12070:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACAGAGCT CTGATTAAAG TG >HWI-ST960:105:D10GVACXX:2:1101:12006:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAGTTGA GCGGTTGAAT AC >HWI-ST960:105:D10GVACXX:2:1101:12122:2230 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTCTGTAT GCTTTTTTGG GAC >HWI-ST960:105:D10GVACXX:2:1101:12107:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCACAAC CTGTGAAAAT CT >HWI-ST960:105:D10GVACXX:2:1101:12066:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTGTGGAT GATGAAGAGT TTT >HWI-ST960:105:D10GVACXX:2:1101:12166:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTGCAATA TTCTAAAGAA CTC >HWI-ST960:105:D10GVACXX:2:1101:12124:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGAATTTGG ATTTGATCAG TA >HWI-ST960:105:D10GVACXX:2:1101:12436:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATAAAGT TAGTTGGTGG TTG >HWI-ST960:105:D10GVACXX:2:1101:12303:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATCTTTCT ACTTTCATTA AC >HWI-ST960:105:D10GVACXX:2:1101:12490:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTTCAATT ATGAGTTTTC CA >HWI-ST960:105:D10GVACXX:2:1101:12308:2196 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTATAGTTA AAAGAGCACT AA >HWI-ST960:105:D10GVACXX:2:1101:12371:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGGTTTGG ACAAAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:12329:2218 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCCTTTGTCG CTAAGATTCG A >HWI-ST960:105:D10GVACXX:2:1101:12376:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTGATCAA GTACAAGGGT TAT >HWI-ST960:105:D10GVACXX:2:1101:12362:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATATC GCATTAGCCC AGT >HWI-ST960:105:D10GVACXX:2:1101:12430:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAATATA CACTGAACTT TT >HWI-ST960:105:D10GVACXX:2:1101:12484:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAAGTTT CTATCAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:12259:2237 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGCCTTGCT CTTCATTGGT TTC >HWI-ST960:105:D10GVACXX:2:1101:12345:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCCCGATAA ATAGAACGAT AT >HWI-ST960:105:D10GVACXX:2:1101:12290:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTGTCTG AAAAAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:12617:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAGTCT TATTGTATCT GT >HWI-ST960:105:D10GVACXX:2:1101:12673:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGATTCA AATCGATCCC T >HWI-ST960:105:D10GVACXX:2:1101:12575:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTTATAT TATGTGAAGT AC >HWI-ST960:105:D10GVACXX:2:1101:12730:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGAGTCG ATCGTAGAGT CT >HWI-ST960:105:D10GVACXX:2:1101:12674:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTTGTTT GATGTCTATG AT >HWI-ST960:105:D10GVACXX:2:1101:12690:2226 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCACTAGCT TCTACTTTGA TAT >HWI-ST960:105:D10GVACXX:2:1101:12653:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTGTTTC TGTCTATGAC TCC >HWI-ST960:105:D10GVACXX:2:1101:12702:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGAGCCTT GTTTCTTATT TT >HWI-ST960:105:D10GVACXX:2:1101:12587:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTATTGA TGATTCTATC TT >HWI-ST960:105:D10GVACXX:2:1101:12614:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCGACATT TGGTGTGAAA TGC >HWI-ST960:105:D10GVACXX:2:1101:12849:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGCCCGACC TCGGACTGGG AAC >HWI-ST960:105:D10GVACXX:2:1101:12894:2184 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAAAGTAGT CTCATCTTAT CAC >HWI-ST960:105:D10GVACXX:2:1101:12816:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTAAAGG CTTATTATCA AAA >HWI-ST960:105:D10GVACXX:2:1101:12946:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTGATGA AATCTCATAT TGA >HWI-ST960:105:D10GVACXX:2:1101:12964:2189 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTAATATAT GGACAATTTG GT >HWI-ST960:105:D10GVACXX:2:1101:12914:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTAA CAACTTTTCA TCT >HWI-ST960:105:D10GVACXX:2:1101:12899:2205 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGAAAGT AGCATCAAAA CAA >HWI-ST960:105:D10GVACXX:2:1101:12750:2211 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATCTAGTA CATACTCTGT TT >HWI-ST960:105:D10GVACXX:2:1101:12962:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTTTGTC TGAGTACGAA CT >HWI-ST960:105:D10GVACXX:2:1101:12876:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATAATT TTTAGTGAAT AAC >HWI-ST960:105:D10GVACXX:2:1101:12908:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTATGAT GTAGAAGTAT TG >HWI-ST960:105:D10GVACXX:2:1101:12760:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGGGCT CTTGTTGTGA ATC >HWI-ST960:105:D10GVACXX:2:1101:12926:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATTCAG CAGGATTATG CT >HWI-ST960:105:D10GVACXX:2:1101:12942:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATTTCAT TGTCTTGTCG GT >HWI-ST960:105:D10GVACXX:2:1101:12902:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTATTTA CATGTTGTTT GG >HWI-ST960:105:D10GVACXX:2:1101:13052:2176 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTTGTGA CTGATCATTA G >HWI-ST960:105:D10GVACXX:2:1101:13197:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTTGTCA CATTGTAAAT CCC >HWI-ST960:105:D10GVACXX:2:1101:13235:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTAATAAG ATTTTCTAGT TG >HWI-ST960:105:D10GVACXX:2:1101:13099:2185 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TTCTCTGTAT CTCTCGACTC TCT >HWI-ST960:105:D10GVACXX:2:1101:13082:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTAGTATTA TTATACACAC TTG >HWI-ST960:105:D10GVACXX:2:1101:13132:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATAAAT AAGCTTTGTT CA >HWI-ST960:105:D10GVACXX:2:1101:13120:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATTTG GACTGAGTCT GT >HWI-ST960:105:D10GVACXX:2:1101:13177:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTACGTC GTTTTGTTCT CTC >HWI-ST960:105:D10GVACXX:2:1101:13060:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATTAAAG AAGAACCCAA AAC >HWI-ST960:105:D10GVACXX:2:1101:13106:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCGTAAAC TCATAAATAA AT >HWI-ST960:105:D10GVACXX:2:1101:13215:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACTGTGTT GGCGTTTTAT CT >HWI-ST960:105:D10GVACXX:2:1101:13012:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAATGCCC ATTAATCGTG GT >HWI-ST960:105:D10GVACXX:2:1101:13172:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTGCCTAT TTATTTGCTG TC >HWI-ST960:105:D10GVACXX:2:1101:13045:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTCTGAG ATTGTAGAAC AAT >HWI-ST960:105:D10GVACXX:2:1101:13155:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCAAAAGGT CAAGGTTGGC AAG >HWI-ST960:105:D10GVACXX:2:1101:13458:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGTAAT GTAGTCTTTT AT >HWI-ST960:105:D10GVACXX:2:1101:13473:2178 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCGTTAGGAC AGTTC >HWI-ST960:105:D10GVACXX:2:1101:13435:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGAATAAT GAACTTTGAT TAA >HWI-ST960:105:D10GVACXX:2:1101:13272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAAATCT CCCTTTTTTT GT >HWI-ST960:105:D10GVACXX:2:1101:13312:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTGTGTAG AATCTGCTTA TAA >HWI-ST960:105:D10GVACXX:2:1101:13253:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TAGTTTGGAC GTTGGTACAC GA >HWI-ST960:105:D10GVACXX:2:1101:13363:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGCTAAGG AAGTAAAAGC CAT >HWI-ST960:105:D10GVACXX:2:1101:13404:2208 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACGACATT GCATTGTATG TTG >HWI-ST960:105:D10GVACXX:2:1101:13366:2209 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATATGTT GTCGGTTCTA GT >HWI-ST960:105:D10GVACXX:2:1101:13340:2212 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATATGTT TCGTAGAACT AT >HWI-ST960:105:D10GVACXX:2:1101:13430:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATGTTTT GGATACATAA AC >HWI-ST960:105:D10GVACXX:2:1101:13478:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATGGTGAT GAAACGAATA TTT >HWI-ST960:105:D10GVACXX:2:1101:13253:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATGGGTC TCTAGATGCT TT >HWI-ST960:105:D10GVACXX:2:1101:13357:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTCTTTG GTGCCCATGC AA >HWI-ST960:105:D10GVACXX:2:1101:13444:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTTACGA TTCATGGTTC TGT >HWI-ST960:105:D10GVACXX:2:1101:13383:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATAATCTC TACTGTTTGT TCT >HWI-ST960:105:D10GVACXX:2:1101:13323:2243 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTCTCAA TACTTTCTTC CTC >HWI-ST960:105:D10GVACXX:2:1101:13556:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTTGTAT AAACGGAATT TCT >HWI-ST960:105:D10GVACXX:2:1101:13647:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCTTGATCA CGAACATAAT ATT >HWI-ST960:105:D10GVACXX:2:1101:13575:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGCTTGCA AGTTCTCTCT GAA >HWI-ST960:105:D10GVACXX:2:1101:13528:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATAGTATG TTTGCGGATT AT >HWI-ST960:105:D10GVACXX:2:1101:13614:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTCTTTC GAGTTTTATG AT >HWI-ST960:105:D10GVACXX:2:1101:13510:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTGTCTTT CTCCTTCTCT TCT >HWI-ST960:105:D10GVACXX:2:1101:13692:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGCTTTG CTTAATTCAT TG >HWI-ST960:105:D10GVACXX:2:1101:13666:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCAAATTT CAATGAGATT GT >HWI-ST960:105:D10GVACXX:2:1101:13720:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATCAGAGT GACTCAACCA AA >HWI-ST960:105:D10GVACXX:2:1101:13526:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGCCCTTT GTCGCTAAGA TTC >HWI-ST960:105:D10GVACXX:2:1101:13506:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATAATGT GTGTGGGACT TA >HWI-ST960:105:D10GVACXX:2:1101:13623:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATGGCAA TCGTCTCTCT AT >HWI-ST960:105:D10GVACXX:2:1101:13684:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGGTC CCCACTGAGA ACT >HWI-ST960:105:D10GVACXX:2:1101:13646:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTGTTA TAGATTCCTC CT >HWI-ST960:105:D10GVACXX:2:1101:13506:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGGAACAA GGATTACAAG AA >HWI-ST960:105:D10GVACXX:2:1101:13700:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATAAGCT GAGCGAATAT TAG >HWI-ST960:105:D10GVACXX:2:1101:13525:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTGTTATT GGCCCAAGTA GA >HWI-ST960:105:D10GVACXX:2:1101:13744:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATGCTCT TTTAATGTGC AT >HWI-ST960:105:D10GVACXX:2:1101:13514:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTTTCAA ACTGAGCAAA AAT >HWI-ST960:105:D10GVACXX:2:1101:13631:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGTTAATG TCTCTGAAAC AA >HWI-ST960:105:D10GVACXX:2:1101:13611:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAACGTAGA AACTCTTGGT AA >HWI-ST960:105:D10GVACXX:2:1101:13873:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGGGGGTCC CAGTTCCGAA CCC >HWI-ST960:105:D10GVACXX:2:1101:13832:2175 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTGC CTTTTTCTCT TCT >HWI-ST960:105:D10GVACXX:2:1101:13756:2181 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGA TCACAGTCGG CTTACCCGGG GAC >HWI-ST960:105:D10GVACXX:2:1101:13888:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGAGAGA TTTCGTAAAA AAC >HWI-ST960:105:D10GVACXX:2:1101:13863:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTGGTTG GTGTAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:13978:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTGACTC TGTAGCTTTA CTT >HWI-ST960:105:D10GVACXX:2:1101:13770:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCAACATAT GTTTCATAAT GT >HWI-ST960:105:D10GVACXX:2:1101:13874:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATAAAAGT TGTCGTAGCA TAA >HWI-ST960:105:D10GVACXX:2:1101:13985:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTCTTGAC TTGCCTCCTT ACC >HWI-ST960:105:D10GVACXX:2:1101:13941:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCTATTTATA TATTTGATGT TT >HWI-ST960:105:D10GVACXX:2:1101:13963:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTCTGTCT ATTTCGTTAA ATC >HWI-ST960:105:D10GVACXX:2:1101:13752:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTTTGTCAA TTGTCATATT TGC >HWI-ST960:105:D10GVACXX:2:1101:13859:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTCTGTTT CAATGTCCCT TGC >HWI-ST960:105:D10GVACXX:2:1101:13939:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAGAGTCAA GACTCAAGAC TAT >HWI-ST960:105:D10GVACXX:2:1101:14180:2173 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCACAACAG CATATTTATA AA >HWI-ST960:105:D10GVACXX:2:1101:14103:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAACAAAAG TGGCTGTAGT TT >HWI-ST960:105:D10GVACXX:2:1101:14196:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAGGTGT TACTGTGGAT TTC >HWI-ST960:105:D10GVACXX:2:1101:14128:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATGTA GTAGCAACTC TT >HWI-ST960:105:D10GVACXX:2:1101:14033:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTGGTAA CTGGACTCTG AT >HWI-ST960:105:D10GVACXX:2:1101:14074:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTAATACA CTTTCCCTTA CAT >HWI-ST960:105:D10GVACXX:2:1101:14019:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTCTCTGT GATTCTCTTT TTA >HWI-ST960:105:D10GVACXX:2:1101:14232:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAGCTGGA AACTTTGAGC TT >HWI-ST960:105:D10GVACXX:2:1101:14143:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTGG CACACTAAGC TG >HWI-ST960:105:D10GVACXX:2:1101:14121:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTAGTAG CATGTGAATT TA >HWI-ST960:105:D10GVACXX:2:1101:14168:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATTCTAT CGGATTCTCA AC >HWI-ST960:105:D10GVACXX:2:1101:14102:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGTATTTG ATCTACATTG TAT >HWI-ST960:105:D10GVACXX:2:1101:14036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCCCGAAC TCTACGTAGA AAT >HWI-ST960:105:D10GVACXX:2:1101:14209:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTACTCAA CACTCTCTTC TT >HWI-ST960:105:D10GVACXX:2:1101:14087:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGAGTTCT TAGCCATTGC AT >HWI-ST960:105:D10GVACXX:2:1101:14127:2230 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCACTCTGGA TTCAATTTGG AT >HWI-ST960:105:D10GVACXX:2:1101:14472:2172 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATAACGA TCCTCTGTGT CTCTCTCGAT CGA >HWI-ST960:105:D10GVACXX:2:1101:14402:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATAAAGT GGTCTAGTGG TT >HWI-ST960:105:D10GVACXX:2:1101:14443:2185 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTTTTACTG TCCTCTGATC AG >HWI-ST960:105:D10GVACXX:2:1101:14420:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATGTAT ATATAAGAGT CAT >HWI-ST960:105:D10GVACXX:2:1101:14467:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGAAACTG TACTTGAGAT TA >HWI-ST960:105:D10GVACXX:2:1101:14311:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTCTTTAT GGCTCTAGTA CAA >HWI-ST960:105:D10GVACXX:2:1101:14442:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAAAATGT CGTTGTAGTA TAG >HWI-ST960:105:D10GVACXX:2:1101:14388:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATTCCAG TTGATTGAGG TC >HWI-ST960:105:D10GVACXX:2:1101:14404:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTGTTG GCTATGATGT TAT >HWI-ST960:105:D10GVACXX:2:1101:14361:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAAATTATG ATGGAAGATT TGT >HWI-ST960:105:D10GVACXX:2:1101:14303:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACATTTAG GCTCAGTGGG A >HWI-ST960:105:D10GVACXX:2:1101:14342:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGCTCTTCA ACCTTAGAAG A >HWI-ST960:105:D10GVACXX:2:1101:14263:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTACTTTC TCGTGCTAAC TC >HWI-ST960:105:D10GVACXX:2:1101:14512:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGCAATCCC TCTGTTTCCT AA >HWI-ST960:105:D10GVACXX:2:1101:14677:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTGACAGA AGATAGAGAG CAC >HWI-ST960:105:D10GVACXX:2:1101:14738:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATGTTCA TGTCTAAATT CG >HWI-ST960:105:D10GVACXX:2:1101:14684:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAGCCGGA GACAGGAGAG GTG >HWI-ST960:105:D10GVACXX:2:1101:14526:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCACATAGAC TAATCTTATA AT >HWI-ST960:105:D10GVACXX:2:1101:14580:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAATAAGG TATCAGGTTT TA >HWI-ST960:105:D10GVACXX:2:1101:14592:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTTATAGG GAGAAGAAGA GGC >HWI-ST960:105:D10GVACXX:2:1101:14659:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATTGGTG CCTGTAGGTC AG >HWI-ST960:105:D10GVACXX:2:1101:14548:2237 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCAATTTTAT GTCGTTTCTT TG >HWI-ST960:105:D10GVACXX:2:1101:14962:2168 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATCCACA CTAAGTCCAA GC >HWI-ST960:105:D10GVACXX:2:1101:14851:2171 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTATTTGTA GCAATTCTGT TTT >HWI-ST960:105:D10GVACXX:2:1101:14982:2172 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCGTAATCTG GGATGAACTC ACT >HWI-ST960:105:D10GVACXX:2:1101:14927:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTCTTGT TTAGAAGCAA GAA >HWI-ST960:105:D10GVACXX:2:1101:14906:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGCCAACTC TGTTTCTTCT TCT >HWI-ST960:105:D10GVACXX:2:1101:14858:2195 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCA TCATTCGTTT CAATGTCAAT CTC >HWI-ST960:105:D10GVACXX:2:1101:14936:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGCCAATG TTGTAGAACT AT >HWI-ST960:105:D10GVACXX:2:1101:14780:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTGTGAA TCCTTTTCCA TT >HWI-ST960:105:D10GVACXX:2:1101:14808:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATGAAGA GGCTGTTTCT AC >HWI-ST960:105:D10GVACXX:2:1101:14828:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATGTATGT TGTTATTTGA TAA >HWI-ST960:105:D10GVACXX:2:1101:14929:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAACACTCT TATCAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:14844:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCATACATCT TTGCAGAACT CAT >HWI-ST960:105:D10GVACXX:2:1101:14988:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGCTTAGA CTTGGTAGTT GT >HWI-ST960:105:D10GVACXX:2:1101:14821:2236 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGTGTACT TGTGGACAAG GT >HWI-ST960:105:D10GVACXX:2:1101:14761:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTTGTAG TCGTAAATAT CT >HWI-ST960:105:D10GVACXX:2:1101:15030:2168 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTCTGTTA CACGCCGAGA TC >HWI-ST960:105:D10GVACXX:2:1101:15079:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCAGGGCA AGCACAACAT AT >HWI-ST960:105:D10GVACXX:2:1101:15143:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCATCTTTTT CATCCCAATC TGT >HWI-ST960:105:D10GVACXX:2:1101:15178:2193 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAGTGATGA ACCTTTTGAA CC >HWI-ST960:105:D10GVACXX:2:1101:15053:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATCCAGT CTCATCGCTG TTG >HWI-ST960:105:D10GVACXX:2:1101:15025:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGA TCGTATGTAA AGGTTTACTC TTT >HWI-ST960:105:D10GVACXX:2:1101:15186:2216 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCAGAGCAAG TCGAAATCTG TT >HWI-ST960:105:D10GVACXX:2:1101:15065:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTGTGCTG GGAACTATTT GAC >HWI-ST960:105:D10GVACXX:2:1101:15143:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATGAAAAC TTCTTGAGTT AT >HWI-ST960:105:D10GVACXX:2:1101:15008:2227 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCTTTCTTGG GACTTGATTT TT >HWI-ST960:105:D10GVACXX:2:1101:15207:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTAGTGT GTAATGTTAT TGG >HWI-ST960:105:D10GVACXX:2:1101:15000:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTGGTCA TGTTTGCTAT TTG >HWI-ST960:105:D10GVACXX:2:1101:15274:2198 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCATCTGTC TAAAGTTTGT TCT >HWI-ST960:105:D10GVACXX:2:1101:15308:2216 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAGTAATTT AGCATGTTGC AAA >HWI-ST960:105:D10GVACXX:2:1101:15475:2222 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCTGTAG TTGTATTTCA AC >HWI-ST960:105:D10GVACXX:2:1101:15291:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGTTG TTAGCTATCA CT >HWI-ST960:105:D10GVACXX:2:1101:15347:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGAACTCT GACCAATGAA CTT >HWI-ST960:105:D10GVACXX:2:1101:15331:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTGTTATA TATTACTGAC TAC >HWI-ST960:105:D10GVACXX:2:1101:15450:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGTTTTGT CCCTTTGTAT TT >HWI-ST960:105:D10GVACXX:2:1101:15691:2179 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTACTAGTC TCGTATTAAC TA >HWI-ST960:105:D10GVACXX:2:1101:15591:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTTGCTT ATGTGCCCGT TTT >HWI-ST960:105:D10GVACXX:2:1101:15612:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATATCCTA TGTCTAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:15528:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATTTCGGA TCTTGGCTAC TAA >HWI-ST960:105:D10GVACXX:2:1101:15503:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAATCTAAA GGGATTTGGT GT >HWI-ST960:105:D10GVACXX:2:1101:15541:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CAAACTTGAA TCGTCTGTAG CTCTAGACCA TTC >HWI-ST960:105:D10GVACXX:2:1101:15700:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTAAATTC TCTTCCTTTG GT >HWI-ST960:105:D10GVACXX:2:1101:15649:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTAATGTGA TGGTTTCTTC AA >HWI-ST960:105:D10GVACXX:2:1101:15573:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATAGCTA GTCATAACTC TTT >HWI-ST960:105:D10GVACXX:2:1101:15731:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATATGTT TCGTAGAACT AT >HWI-ST960:105:D10GVACXX:2:1101:15639:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTTTTACG GAGTACAAGA GAT >HWI-ST960:105:D10GVACXX:2:1101:15824:2174 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATATGTC TGTACACAAT CT >HWI-ST960:105:D10GVACXX:2:1101:15924:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGAAA ATGTTGTGAA CTG >HWI-ST960:105:D10GVACXX:2:1101:15857:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTAGGTT TAGAGCTAAA AAA >HWI-ST960:105:D10GVACXX:2:1101:15755:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATACTA CTAATACATT TT >HWI-ST960:105:D10GVACXX:2:1101:15970:2220 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCCATGACTG AAGTTGTTTG TC >HWI-ST960:105:D10GVACXX:2:1101:15886:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTGTTTT ATTTCTTATT CAA >HWI-ST960:105:D10GVACXX:2:1101:15866:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTGTGTTG GCGTTTTATC TG >HWI-ST960:105:D10GVACXX:2:1101:15925:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTTTTGTT GGATTGTTTT GCT >HWI-ST960:105:D10GVACXX:2:1101:15938:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTCTTGTCC GTTACATTTG CC >HWI-ST960:105:D10GVACXX:2:1101:16016:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTGTGTT GGCGTTTTAT CTG >HWI-ST960:105:D10GVACXX:2:1101:16084:2189 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAAATGTGA AATCTTAAAA TC >HWI-ST960:105:D10GVACXX:2:1101:16060:2193 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCGAGAATGA TGAACCAATT AC >HWI-ST960:105:D10GVACXX:2:1101:16022:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCATGAGAT ACTGAATTCA AGC >HWI-ST960:105:D10GVACXX:2:1101:16131:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTATGTAT GATCATATTT TT >HWI-ST960:105:D10GVACXX:2:1101:16147:2216 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCATTCAAAT CAGAGGCTTG TTA >HWI-ST960:105:D10GVACXX:2:1101:16171:2218 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTCTTCTTC GTTTGGCTAT TTT >HWI-ST960:105:D10GVACXX:2:1101:16114:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGCAGCAC TTGTCTGACC CAT >HWI-ST960:105:D10GVACXX:2:1101:16083:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATGTAGA GAATCGATTT AT >HWI-ST960:105:D10GVACXX:2:1101:16174:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCACTTTGAG AACTAAAAAA AA >HWI-ST960:105:D10GVACXX:2:1101:16002:2242 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGGAGTTT TGGTTAGGTT GT >HWI-ST960:105:D10GVACXX:2:1101:16214:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTGGTAG ATGATAACAA ATC >HWI-ST960:105:D10GVACXX:2:1101:16126:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTGTTGT TGTTGTTGTT GT >HWI-ST960:105:D10GVACXX:2:1101:16191:2247 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCTGGAGAAC TTGGCAACTC AC >HWI-ST960:105:D10GVACXX:2:1101:16438:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATGTTCGG TTGTGGGATT CT >HWI-ST960:105:D10GVACXX:2:1101:16355:2177 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTTA GACTCTTCGA TTT >HWI-ST960:105:D10GVACXX:2:1101:16306:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTACCTACT CGTCGTACAT TTT >HWI-ST960:105:D10GVACXX:2:1101:16427:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGTTGATTT TAATGGTTAC TGT >HWI-ST960:105:D10GVACXX:2:1101:16368:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATAAAAAC TCTGAATTTA AT >HWI-ST960:105:D10GVACXX:2:1101:16496:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTTCTGTTG AACCTCTTG >HWI-ST960:105:D10GVACXX:2:1101:16268:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTCAAACC ATTGAGACAG CTT >HWI-ST960:105:D10GVACXX:2:1101:16478:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCCTGTGAAA CTGCGAATGG CT >HWI-ST960:105:D10GVACXX:2:1101:16378:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTACGTTA TTTAAAATCC TC >HWI-ST960:105:D10GVACXX:2:1101:16273:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTTATGT GACTGGAGAG A >HWI-ST960:105:D10GVACXX:2:1101:16350:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTGTGGCT CAGAACCACC AC >HWI-ST960:105:D10GVACXX:2:1101:16328:2230 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAA TCACTGATCG CGTCGTGTTA C >HWI-ST960:105:D10GVACXX:2:1101:16408:2232 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTCGAAC AATGAACAAT TGC >HWI-ST960:105:D10GVACXX:2:1101:16369:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTACATTGT GAAATGATAT TTC >HWI-ST960:105:D10GVACXX:2:1101:16305:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCAAACCTG TATCTGTGTA ACT >HWI-ST960:105:D10GVACXX:2:1101:16647:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTAATTGAA TATCTTCAAT GT >HWI-ST960:105:D10GVACXX:2:1101:16734:2178 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTACGAAT TCTAAATTTT AT >HWI-ST960:105:D10GVACXX:2:1101:16682:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTATCAATA AGCGGAGGAA AAG >HWI-ST960:105:D10GVACXX:2:1101:16516:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGAGAGTTC GAATCTGTCA GGC >HWI-ST960:105:D10GVACXX:2:1101:16583:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATCGGCGC TTGTTCACCT CTC >HWI-ST960:105:D10GVACXX:2:1101:16633:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCATTGTATT TTAACAGCAC TC >HWI-ST960:105:D10GVACXX:2:1101:16696:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTAAT GTAGTCTTTT AT >HWI-ST960:105:D10GVACXX:2:1101:16666:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTAACAC TTGGTTCCGT TTC >HWI-ST960:105:D10GVACXX:2:1101:16730:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCCTATAAA TCGTCTCATG AA >HWI-ST960:105:D10GVACXX:2:1101:16561:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATAACCCT TTCCAGGCCA TGT >HWI-ST960:105:D10GVACXX:2:1101:16708:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCACCATTG TCTGAATAAA AAG >HWI-ST960:105:D10GVACXX:2:1101:16847:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCGATGTCGG CTCTTCCTAT CAT >HWI-ST960:105:D10GVACXX:2:1101:16809:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACATCCTC ATAATCACTT TC >HWI-ST960:105:D10GVACXX:2:1101:16946:2180 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTCTTTTG TCGGCGTTAG GT >HWI-ST960:105:D10GVACXX:2:1101:16831:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTATGTTAT GGATTCAAAA AAA >HWI-ST960:105:D10GVACXX:2:1101:16770:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTCAGCCCT TTGTCGCTAA GA >HWI-ST960:105:D10GVACXX:2:1101:16858:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAATTTTTA GTGACCCTTT TA >HWI-ST960:105:D10GVACXX:2:1101:16876:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATGTTC TCTGTTATTC TC >HWI-ST960:105:D10GVACXX:2:1101:16983:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCCTTTGTGG GTTGAGTTGT CT >HWI-ST960:105:D10GVACXX:2:1101:16842:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTATGAAA TCGACCATGA CA >HWI-ST960:105:D10GVACXX:2:1101:16962:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTCATGCT GTTTTCCAAC AGC >HWI-ST960:105:D10GVACXX:2:1101:16751:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTACTGTT TTCTGTTTTC TT >HWI-ST960:105:D10GVACXX:2:1101:16898:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCAACCCCCG AACTATATCC TC >HWI-ST960:105:D10GVACXX:2:1101:16969:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCATTATCTT GTAGAATGTT CA >HWI-ST960:105:D10GVACXX:2:1101:16781:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTTCTCCT CTCGTCCATA AAT >HWI-ST960:105:D10GVACXX:2:1101:17222:2169 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTGGATCCT GTTTTGGATT GT >HWI-ST960:105:D10GVACXX:2:1101:17028:2180 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATA TCCTATTTAC TATTTGAAAA AGC >HWI-ST960:105:D10GVACXX:2:1101:17127:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCAATTGGAC TGTTTAACGT TT >HWI-ST960:105:D10GVACXX:2:1101:17143:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCAAATTTCT ATATATTGTT TT >HWI-ST960:105:D10GVACXX:2:1101:17161:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCTTCTGGAC ATTAGCCATT AGT >HWI-ST960:105:D10GVACXX:2:1101:17133:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCTGCCTTTT CCTTCTTGTC GG >HWI-ST960:105:D10GVACXX:2:1101:17121:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGGCACTTC TGTTCTGATC CT >HWI-ST960:105:D10GVACXX:2:1101:17033:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCACTAGACA AACTCTCAAG A >HWI-ST960:105:D10GVACXX:2:1101:17178:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGTTTGTAG TCATAATTTA GT >HWI-ST960:105:D10GVACXX:2:1101:17141:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGA TCGTATGTTT CACTCTGTAA CT >HWI-ST960:105:D10GVACXX:2:1101:17119:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCGAGACCAG ATGTGCGATG TTT >HWI-ST960:105:D10GVACXX:2:1101:17246:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAA TCATTTGGTT AGGTCCTTTG TTC >HWI-ST960:105:D10GVACXX:2:1101:17011:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTTTTGAGG TTTTAAGATG TT >HWI-ST960:105:D10GVACXX:2:1101:17469:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCA TCTGTGTTGG TGAAGGAAGG AAC libqes-0.1.21/test/data/test.fastq000066400000000000000000004315461263611052100167730ustar00rootroot00000000000000@HWI-ST960:105:D10GVACXX:2:1101:1151:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAANGACATTGAATCTATATGT + JJJJJJJIJHIJCC#4ADFFHHHGHJJJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:1205:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGNATTCTTCTTTTGGAACTC + JIJIJJJJJIIIBC#4ADDDHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1122:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCAGTTTAAAGTTAACTCATTG + JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1229:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTGAGTTTTTGGACTGTACAT + IJJJJJJJJJJJCCCFFDFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1175:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTAATTGTCACTGTTTCACCC + IJJHHIJJJJJJCB@FFFFFHHHHHJJJJJIGJ @HWI-ST960:105:D10GVACXX:2:1101:1175:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTGTGACTCTGTTCCTGTTGT + IJJJJJJJJJJJ@BCFFFFFHHHHHIJJIIJJJ @HWI-ST960:105:D10GVACXX:2:1101:1204:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATCACAGAGCAGCAGTATTTC + IJJJJJJJJJJJCCCFFFFFHHHHHJJHIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1237:2239 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTACACACGTATATGCAATAC + IJJJJJJJJJJICCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1123:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATAATGTGGTATTAGTCTG + JJJIJJJJIJJJBCCFFFFFHHFHHJIJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:1155:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAGCCACTGAACTAAAAAAAAA + HFFFFFEEEEEECCCFFFFFHGHHGJJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:1466:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGNAAACGCATGTAGATGAT + JJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1443:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTACCAAAGTCTGAATGATTAT + IJJJJJJJJJJJCCCFFFFFHHHHGJIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1360:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCCGGCTCTGTCTCTCTCTCCC + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATCATTTAGAGGAAGGAGAA + JJJJJJJJJJJJCCCFFFFFHHHHHJJJIIJJ @HWI-ST960:105:D10GVACXX:2:1101:1423:2185 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATGACGTCAAATTATGCCT + JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:1398:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAAAAAAAAAAAGAATAAAGAA + C@CBBAABCCCC@@@DDDDDHHFDFIBFHGF @HWI-ST960:105:D10GVACXX:2:1101:4487:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAAATTGTTACGCAACAAACT + HFI85DDBCEHH@@>@ @HWI-ST960:105:D10GVACXX:2:1101:4599:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTGTTATCGTGTCTGTAAGC + JJJJJIJJJJJJ@@@DFFFFDHHBHIIJGJGB @HWI-ST960:105:D10GVACXX:2:1101:4699:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTGCCTTCAAGTTAACTTTGT + GIIHIHIJIJJJ@@BFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:4615:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGTCTTCTTCTTCTGTATTA + DBGDEHGIGG@C@@@FDDFDDFFHFHBAGDII @HWI-ST960:105:D10GVACXX:2:1101:4505:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATCCTATGCTTTGGTCATAT + IIIGIGGGGIII@@?DDADDH?FHFEDFHFFFFGIIJJII @HWI-ST960:105:D10GVACXX:2:1101:7292:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTCAATCCATGGTTTTCTCAAAGTTTTC + HJJJJJJJJJJJCCCFFDFFHHHHHJJJHIJJJ @HWI-ST960:105:D10GVACXX:2:1101:7393:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATGTCTCTGTACTGTAAC + JIJIJJJJJJJJC@BFFFFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7359:2210 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGATCAGAGATCGGAAGAGATGGCTT + JFGGHHJJGEHH@C@FFFFFHGHAFGIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7415:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTAATTATTCGTATGAACT + IIJIJJJJJJJJ@@CFFFFFHHFHHJJIIJJJ @HWI-ST960:105:D10GVACXX:2:1101:7403:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCGTCTTACCATTTCTTTCAT + III@=F4./@FI@@@A?DD>AC>BF@GFGBHI @HWI-ST960:105:D10GVACXX:2:1101:7373:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATGTCTGTCTAGTCTATTG + IHIGIJIJJJIJ@CCFFFFFHHHHGHIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7324:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATCAAATGTATTATATATAT + IJJJJJJJJJJJC@CFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7309:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTGAGTTTTTACATGTTTGT + IIJJJJJJJJJJ@BBFFDFFHHHHHJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7475:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTTGACTGTATTGAGCAACC + IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7687:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTNTAGTCTAAGGCTTTTCAA + HIJJJJJJJJJJCC#4BDDFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7649:2170 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTGAGTAGACAATTTAATCA + F?B@FHGIJGEH@@@FADEFHHHFHJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:7708:2170 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGTTTAATAAAACAGAACAA + IJJJJJJJJJJJCCBDFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7709:2191 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTCTCTCTCTTACCTTTCTCT + JJJJIJJIJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7690:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTCGATTAGTACCGTTAGTG + IIIEIHIJJIHHCCCFFFFFHGHHHJIHIIJIG @HWI-ST960:105:D10GVACXX:2:1101:7607:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCCCGGAATGGTGCCTTTGTTAC + HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7698:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCCTCTGGCTTTGCTCAGATTT + IJJJJJJJJJJJ@BCFFFFFHHHHHJJJIIJJ @HWI-ST960:105:D10GVACXX:2:1101:7518:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCAATTCTTTTACCGGGTTGAG + HHIJHJJJJHHHCCCFFFFFHHHHHJJGHJJJ @HWI-ST960:105:D10GVACXX:2:1101:7534:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATAATGAATGTTTCGGACTTC + FFGIJIEHIJGH@CCFFFFFHHHHHJJIGIIJG @HWI-ST960:105:D10GVACXX:2:1101:7679:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATCGGTGAGTGGAACTTCTT + IJJJJJJJJJJJBCCFFDDDHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7747:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCCACGAGTCGAGGCTCTCAATA + HJJJJJHHHHHHBCCFFFDFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7610:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTCAGTGGTAGAGCGCGTGGC + HHHHHFFFFFFECCCFDFFEHHHHHJJJHIJJ @HWI-ST960:105:D10GVACXX:2:1101:7532:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTATGTTCACTGTTCTCTGC + DBFFCCFHGGEG?@CFDDDDHHHHHGGJJGIJ @HWI-ST960:105:D10GVACXX:2:1101:7676:2238 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCCAGCCGTCGGATACTGACTT + IIIIIHHACHHF<@@FFFFDHHHHHDDHIIII @HWI-ST960:105:D10GVACXX:2:1101:7641:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATCTGTAGCCTCTCTTTTAGT + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJH @HWI-ST960:105:D10GVACXX:2:1101:7824:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNAGTCTCTTTTTTGAATT + GGHDHHIEGHGH@@#4=ADBFHHHGIIGIGGI @HWI-ST960:105:D10GVACXX:2:1101:7876:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAANACATGGGAAAATATGTG + ==='566A@===@@#442AAAD?CB?C@G>IB @HWI-ST960:105:D10GVACXX:2:1101:7774:2165 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTCNAACGAGGAAAGGCTTAC + JJJJJJJHHHHFCC#4ADFFHHHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7839:2165 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTNTAAAACTGTGCCATTAT + IJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7920:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAANTTCTTTATACTTTGTAAA + HIJJJJJJJJJJCC#4ADFFHHHHHJJJJHIJJ @HWI-ST960:105:D10GVACXX:2:1101:7966:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATGCAACTGCAAATTCTGCA + JJIJJJJJJJJJCCCFFFFFHHHHHJJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:7948:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTTGCTGTGGATGATCTGGT + HIJJIJJJJJJJ@CCFFFFFHHGHHJJJJJJH @HWI-ST960:105:D10GVACXX:2:1101:7864:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCGGAAGAACTCTGGAAGTGAA + JJJJJJJJJJJJCCCFFFFFHHHHHJJJHIJJ @HWI-ST960:105:D10GVACXX:2:1101:7912:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAACAAGATGTTTAATCATCC + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7970:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCACAATTGTTGTCTTGTAGTA + IIJGHJJJIIGJ@C@FDFFFHHFFAHIHIJHH @HWI-ST960:105:D10GVACXX:2:1101:7819:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTAATTGTTTCTTAGCATCT + IJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7762:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTACTTTATAAGGACTGTGAA + IJJIJIJJJJJJCCCFFFFFGHHHHJJJIIJJ @HWI-ST960:105:D10GVACXX:2:1101:7847:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATGCAACCCTGTCTTGCTTTA + IJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7775:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTATTGTGTTACTGAATCTT + JJJJJJJIJJJJCCCFFFFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7900:2219 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTACGCCCGAACGCAAACC + HFFFFDDDEDDDCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7800:2227 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCTCTTATGATGTCAAAACTTTC + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7973:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTATGTGTTCTGCAGATCGA + IIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7844:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTTCGTTGGGTTTTCTTCAT + IIJJJJJJJJJJ@BBFFFFFHHDHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:7863:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATAAATTTTCGAAGGAGACAA + HIJJJIJJIJIH?BBFFFFFHHHHHJIJJIGII @HWI-ST960:105:D10GVACXX:2:1101:7912:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCGTGTGTAACCTCATATGGAC + IIJJGIJJJJJJCCCDFFFFHHHHHJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:7940:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCGTGTCAAGTGTAGAATCAA + IJJJJJJJJJJJBBBDDFFFHFHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8088:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCCANTGGAAGGCTGTGGAGGA + IJJJJJJJJJHHCC#4ADFFHHHHHHIIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8140:2163 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCCGNTGGGTTGGGGATCCGGT + HEHE@DBDBCCC@@#4ADB=?DDDHIAFBE@? @HWI-ST960:105:D10GVACXX:2:1101:8156:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATNTGTAAGTATGAACAAAA + IIIIJJJJJJJJCC#4ADFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8057:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGNAACATTGAACAAGCAGTT + IJJJJJJJJJJJCC#4ADDFHHHHHJJJJIJIJ @HWI-ST960:105:D10GVACXX:2:1101:8023:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATGTATCTTGTTGTTTATCTA + HIJJJJJJJJJJCCCDFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8157:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTCAGTGGTAGAGCGCGTGGC + EHHFHHFFFFFF@BBFDFFDFHGHHJIJIIJI @HWI-ST960:105:D10GVACXX:2:1101:8117:2186 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCATCACTGAATCGACTTTGGGCAAA + HJJIIHFHIJJJCCCFFFFFHHHHGGIJJIIJJ @HWI-ST960:105:D10GVACXX:2:1101:8197:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATGGTGCTTAAAAAAAAAAA + C;@>BBDDACCA@CCFDEFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8236:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATGTCGGCTTAAACTCTAT + FGIIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8088:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATGGAAATGTGCTATGGAC + JJJJJJJJJJJJCCCFFFFFHHFHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8085:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTCGCAGTCGCTAAGCGTCAC + JJJJJHHHHHHFCCCFFFFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8003:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATATTTGTGGATGATGAAGA + IIJJJJJJJJJJCCCFFFFDHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:8138:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTATATGATTCTACTTAGTCA + IJJJJJJJEIJICCCFFFFFHHHHHJJJJJIIJ @HWI-ST960:105:D10GVACXX:2:1101:8069:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGGTACTATGAACATTGTGAC + HGIIGGIGHIII@CCDDFFFHHGHHJJJIIIJJ @HWI-ST960:105:D10GVACXX:2:1101:8445:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNAGATTAGACTCTGTTTGC + IJJJJJJJJJJJCC#4ADFFHHHHHJJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8271:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCTNTGTATAATTGGAACAAG + HIJHGIJIHIGIBC#4=ADFHHHHHJIJIJIJ @HWI-ST960:105:D10GVACXX:2:1101:8390:2167 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTNCGTGTAGAAGGGAAATGA + IJJJJJJJIJHHCB#4ADDFHHHHHJJJJJIII @HWI-ST960:105:D10GVACXX:2:1101:8355:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTATGTGTAACCCTGTCCTT + IJJJJJJJJJJJCCCFFFFEHHHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8375:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATATTGCTATAGAGTCACGCATCT + IJJJJJJJIJJH@CCFFFFFHGGFHIIIGIJII @HWI-ST960:105:D10GVACXX:2:1101:8257:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCACCTGGAGACTCATGTGTTGA + IJJJJJJJIJJIBCCFFFFFHHHHHJJIJJJJI @HWI-ST960:105:D10GVACXX:2:1101:8438:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTTGGTTTGGATTTTGGTTA + IJJJJJJJJJJJCCCFFDFFHHHHHJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:8299:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATCTCTGGCTGTTGAATAGA + IJJJJIIJJJJJCCCFFFFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8333:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGCTTGCAAGTTCTCTCTGAA + HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8309:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCACTGTGTTGGCGTTTTATCTG + IJJJJJIHFHHH@CCFDFFFHHGHHJIIJIJJI @HWI-ST960:105:D10GVACXX:2:1101:8363:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCAAGCATGATGAATTGATGAG + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8494:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTTTGCATTGATTGTGGTTAC + HIJJJJJJJJJJCCCFFFFFHHGHHJIJIGGJJ @HWI-ST960:105:D10GVACXX:2:1101:8291:2212 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCTCTACTCTACTAAACCTCTGT + IJJJJJJHIJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8482:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATCTTCCGTCTGTTTCTGAT + HGIHIIJIHHGICCCFFFFFHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:8322:2218 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCTTGACCGATGCTCGGACAA + HGHHHHHFFFFECCCFFFFFHHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8388:2225 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCGTGTGTATTTAGTAATTCAT + JJJJJJJGIJIJ@B@DDEFFHHHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8442:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATTTTCTATGTTGTTTGGTAG + HIJJJJJJJJJJCCCFFFFFHHHHHIJJJJFII @HWI-ST960:105:D10GVACXX:2:1101:8339:2233 1:N:0: bcd:RPI2 seq:CACCGATGTATC CACCGATGTATCATCTCTAGAACTCTTTATAAT + HIJJIJJJHIJJCC@FFFFFHHHHHJJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:8376:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATGTGTCAGATTCTAAAAAA + IIIIIHHIIIII@@CDFFDFHFDHHBHGIIII @HWI-ST960:105:D10GVACXX:2:1101:8457:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCACTCTGTGGATTATGCTTTA + IGIJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8675:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNTAGTAGAATTGGTTGCAT + IGIIIIIIIIII@@#4ADDDHHHHHIIGIIIII @HWI-ST960:105:D10GVACXX:2:1101:8657:2165 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCGANCGTTTCTCTAGTTTTGT + IIJJGJJJJJJJCC#4ABDDHHHHHJHIJJJG @HWI-ST960:105:D10GVACXX:2:1101:8627:2171 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGGTAAATTTGTCTGAATTA + JIJJJJJJJJJJBCCBDFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:8743:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATCATCTTTTCTTATGTAAA + JJJJJJJJJJJJCCCFFFFFHHHHHJJIHHJG @HWI-ST960:105:D10GVACXX:2:1101:8722:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATGTAGAGAAAGTGATTA + IIJJJJIIJJIJCBBFFFFFHHHHGJHH?GCEHG@?@DDBBDBHHFHGIIIGEHI @HWI-ST960:105:D10GVACXX:2:1101:10530:2160 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCCTNGTGATCATGAAAAAAAA + IHHGHHF@CFFFBC#4=DDFHHHGHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10666:2165 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTANCTCTCCAGTTTGTCATCT + FHHIIJHEEHGI@C#4ADDFHHHHHJJGHGGHJ @HWI-ST960:105:D10GVACXX:2:1101:10737:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTNTGCTTATGTGCCCGTTTT + JJJDHIJHHHHHCC#4ADDFHHGDHIJJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:10690:2167 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATNTAAATTTCGGAAATGCT + JJJ>@GHGGHHHCC#4ADDFFHHGFGIGGIIJ @HWI-ST960:105:D10GVACXX:2:1101:10707:2172 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATTTAAATTCCTTCAAGT + JJJJJJJJJJJJCB@FFFFFHHHHGJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10553:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTATGTGTAGACTTAATTTTTT + HIJGIHHHFFFF@CCFDFFFHHHHHIIJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:10597:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTAATGTACCGATGCATAGTC + IJJJJJJJJJJJBBCFFFFEHHHHHJJJJJJHH @HWI-ST960:105:D10GVACXX:2:1101:10566:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTAGTTTTTGGATTGTAAATT + IJJJJJJIJJJJCBCFDFFFHHHHHJJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10694:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTTGTAATGTTAAATAACTC + HIJIJJJJJJJJBB@FFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10746:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTAACAGGGACAGTCGGGGGGT + DDDDDDDDDDDDCCCFFFFFHHGHHIIJJJJD: @HWI-ST960:105:D10GVACXX:2:1101:10522:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTCTGTACAGATATACTTTTT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10609:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTTGGCTTTTCTCTGCT + GIJGIJJJJIJJCCCFFFFFHHHHHJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10672:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTGGACTCGGATACGCTTCA + IIJJJJJJJHHH@CCFFFFFHHHGHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10584:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGATGTTGAGGCTCAAAAGTT + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJIII @HWI-ST960:105:D10GVACXX:2:1101:10743:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTCGATAGAACTACAAAGAAT + IJJJJJJJJJIJCCCFFFFFHHHHHJJJIIIJJ @HWI-ST960:105:D10GVACXX:2:1101:10653:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGTCCTTCGGATCACTCAAT + IIJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10642:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGATTTTAAAGTGTTACAAG + IJJGEIJIIJIJ@C@DDFFFHDDHHGGJIIJG @HWI-ST960:105:D10GVACXX:2:1101:10627:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAACAAGTTGGTCTGGGTTGT + IJJJJJJJJGHHB@@FFFFDFFDFFIIJFGHG @HWI-ST960:105:D10GVACXX:2:1101:10734:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTAATCTGGGATGAACTCAC + HEHIIGIJJJJJC@CFDFFFHHHHHIIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10579:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATCTTTAGTAGAACAAAATC + IIJGIJIDIJJJ@CCFFFFFHFFFHIGHIIJJJ @HWI-ST960:105:D10GVACXX:2:1101:10596:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGGTACTAATGGCGAAAGAAC + IIJJJJJIIHHH@C@DFFFFHHHHHJJJGGGI @HWI-ST960:105:D10GVACXX:2:1101:10939:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCANTAATTCCCTCTGATTCAT + HHHIIJGIJIJJ@@#4ADDFFHHHFGHJJJGJJ @HWI-ST960:105:D10GVACXX:2:1101:10984:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATTACGATGTCTCTGTACTC + IJJJJJIJJJJJCCCFFFFFHGHHHJJGHIJJ @HWI-ST960:105:D10GVACXX:2:1101:10870:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATGGGTTCGACGTTAAAAAA + JJHHHHHFFFFFBCCFFDDFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10979:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAACTGAAATGAACCAAAACC + HHIIIIIICEGHCCCFDFFFHGFHHJJJJJJH @HWI-ST960:105:D10GVACXX:2:1101:10780:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTGGTGGAACTACATTATC + JJJJIJJJJJJJCCCFFDFFGHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:10858:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGTTTGCGGATTATGCGTTTT + HHHHHFFFFFFECCBFFFFFHHHHHJJJJFGIJ @HWI-ST960:105:D10GVACXX:2:1101:10924:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAACAAAGTCGTTGTAGTATAG + JJJJJJJJJIJJCCCFFFFDHHHHHHIJFHJJI @HWI-ST960:105:D10GVACXX:2:1101:10881:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCATACTGTGTCTGCTTCTAT + IGIIIIIGGHII@@>C@@@FDDBDFFHGGIIIIJHGH @HWI-ST960:105:D10GVACXX:2:1101:11259:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAATATGTTTCGTAGAACTAT + IIIJGIJJJIJJCCCFFFFFHHHHHIJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:11401:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTGTAGAAAATGAACTATAAAT + IJJIJJJJJHIJCCBFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11352:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTGAATAGTCGGGGTTACTT + IJJJHHHHFDFFCCCFFFFFHHHHHJJHIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11437:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTGCGTCGTATGAGTAAAAG + JJJIJJHHHHHF@CCFFFFFHHHHHIJGIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11258:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAACCGAGTACTTTTGGTAGC + HIJJHIJIJJJJ@BBFFFFDHHHHHJJJFHIJ @HWI-ST960:105:D10GVACXX:2:1101:11443:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATGTAGTGTAGTGGTAAAA + JGIJJJJJJJJJ@CCFFFFFHHHHHIJFHJJJ @HWI-ST960:105:D10GVACXX:2:1101:11272:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAGTGCTTCAACGGCTCTGGT + HIJJJJJJHHHH@@@DDFFFHGHFHIHGIIJH @HWI-ST960:105:D10GVACXX:2:1101:11399:2247 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCATATGAACTACGTGTGGCTT + JJJIJIJGIIJJCCCFFFFFHHHHHJHIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11695:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAGNGCTTCCTAGAGCAAAGGA + IJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJHJ @HWI-ST960:105:D10GVACXX:2:1101:11611:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAGGAGCTCAAGAACGGAAGAT + IIJJJJJIJJHHCCCFFFFFGHHHHJJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11736:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGAATACTGTGGTTGTTTTAG + JIJJJJJJJJJJCCCFFFFFHHHHHJHIJJJI @HWI-ST960:105:D10GVACXX:2:1101:11736:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTGATACAATTTCGGTTTCGT + JJJIJJJJJHHHC@CFFFFFHHHHHJHIJJIH @HWI-ST960:105:D10GVACXX:2:1101:11623:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTGTTTTGGGGTTTTAAACAT + IJJJJJHHHHFFCCCDFFFFHHHFHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11724:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTTAGGACAGTTCATGTTTTT + JJJJJJHHHHHFCCCFFFFFHHHHHJJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11676:2225 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGCATCAAGCTGTAACCGAAC + HJJJJJIJJHHHCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11707:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGGTATGAACTATGAACACAA + IJJJJJJJJJJJCCBDFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11640:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTTGTTAGACTCTTCGATTT + HHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11532:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCACTAGTAATAGAGCTTGGAA + IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11511:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATTGGAGATATTGGTTAACT + IJJJJJJJJJJJCCCFFFFFHHHHHJIIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11573:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAACAATTCGGCTAGAAATTT + IGIJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11924:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNCGTCGTTGTAGAATATC + IIIJJJJJJJJJCC#4ADDFHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:11984:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCACNACCATCTCTGAACTCAT + JJJJJJJJJJJJCC#4ADFFHHHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11822:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTNATTTTTTCTTGCAACAC + JJJJJJJHHHHHCC#4ADFFHHHHHJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:11773:2169 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTTTCTTACTTCGGCCTGTT + JJJIJJJJJHHHCCCFFFFFHHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11943:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAAGATCATATGGACGTAACAT + IJJJJJJJJHJHCCCFFFFFHHHHHJJJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:11759:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATTGAGCTCTTCTTTTCTTA + JJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11857:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTCTGTAGTAGGCTTGCATGC + HHIIJJIIJJJICCCFFFFFHHHHHJJJJJJEH @HWI-ST960:105:D10GVACXX:2:1101:11838:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATCAATGTATTGTATCCG + IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11790:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGAATTTCTGTAGACTATGT + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11770:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGGATGCGATCATACCAGCAC + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:11869:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCTGATGTTGGTTTGTAATAT + IJJJJJJJJJJJBCCDFFFFHHFHHJIJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:11959:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTACTGTACACACAAACTTC + JJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11892:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATAAAATGACTCTGAAAAA + JJIJJJJJJJJJBCCFFFFFGHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:11899:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTATAATGTAATAGTACTCACC + IJJJJJJJJGHJ@BCFFFFDHHHHHHIJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:12145:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGNTTCCGTTCCTGTTATCT + III<==8=8@DI?<#4=BDD:F?DFACB?C?E @HWI-ST960:105:D10GVACXX:2:1101:13444:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTTACGATTCATGGTTCTGT + IHICBFHGIIII<@@FFBDDHDDHHGEHHBG?A @HWI-ST960:105:D10GVACXX:2:1101:13383:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATAATCTCTACTGTTTGTTCT + FHIGIIGAGEHICC@FFFFFHHHGFHIGHCFEE @HWI-ST960:105:D10GVACXX:2:1101:13323:2243 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATTCTCAATACTTTCTTCCTC + HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13571:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTNTGTAGAATAAAGCTCTCT + IJJIJIIJJJJJCB#4ADDDHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13621:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNATATACACTGAACTTTT + JIJJJJJJJIJJCB#4ADFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13664:2164 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCTTNCGTCGACTATGATTAAT + JJJJJJJGIJJJCC#4ADDFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13556:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTTTGTATAAACGGAATTTCT + HIJIJJJJJIJJCCCFFFFFHHHGHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13647:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCCTTGATCACGAACATAATATT + HIJJJJJJJJJJCCCFFFFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13575:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGCTTGCAAGTTCTCTCTGAA + JJJJJJJJJJIJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13528:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATAGTATGTTTGCGGATTAT + IIJJJJJJJJJHB@BFDFFFHHHHHJJGIIJJ @HWI-ST960:105:D10GVACXX:2:1101:13614:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTCTTTCGAGTTTTATGAT + JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:13510:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTGTCTTTCTCCTTCTCTTCT + JGIJJJJIJJJJCCCDFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13692:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTGCTTTGCTTAATTCATTG + HIJJJJIJJJJJC@BFFFFFHHHHHJJJJJJH @HWI-ST960:105:D10GVACXX:2:1101:13666:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTCAAATTTCAATGAGATTGT + IJJIJJJJJJJJCCCFFFFFHHHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13720:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATCAGAGTGACTCAACCAAA + IJJIJIIJJJJJBCCFFFFDHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13526:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGCCCTTTGTCGCTAAGATTC + JJJFJJJJIGFHCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13506:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAATAATGTGTGTGGGACTTA + FHIIIIIIIIII@@@DDDD;CCFF;GFHHAEH @HWI-ST960:105:D10GVACXX:2:1101:13623:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAATGGCAATCGTCTCTCTAT + IIJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13684:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATGGTCCCCACTGAGAACT + IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13646:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTTTGTTATAGATTCCTCCT + IJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13506:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAGGAACAAGGATTACAAGAA + HIJJJJJJJJJJC@CFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13700:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTATAAGCTGAGCGAATATTAG + IJJIJIJJHHHHCCCFFFFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13525:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTGTTATTGGCCCAAGTAGA + HDHIIIJJIJGI@CCFFFFFHFFHHJIGCGGH @HWI-ST960:105:D10GVACXX:2:1101:13744:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTATGCTCTTTTAATGTGCAT + IJJJJJJJJJJJCCCFFFFFHHHHHJJHJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13514:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTTTCAAACTGAGCAAAAAT + F=FDGIHGHGHG@@@DFDBDFHHDD:ACFHGHI @HWI-ST960:105:D10GVACXX:2:1101:13631:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGTTAATGTCTCTGAAACAA + IJJIJJJJJJJJCCBDFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13611:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAACGTAGAAACTCTTGGTAA + JJJJJIJJJJJJCCCFFFFFHHHHHJJJJHIH @HWI-ST960:105:D10GVACXX:2:1101:13895:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTNATGTTGGCAAAGAAACAC + IJJGIGHHJHHH@@#4ADDDHHHHFJGHIJIHH @HWI-ST960:105:D10GVACXX:2:1101:13803:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCACNGTGTTGGCGTTTTATC + IGIJJIJJJJHHCC#4ADDFHHHHHIJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:13821:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTNCGTTCTCTGTTGATGAC + F=F;FADEEHGC@@#4=DDDFFHHFIF>C?EF @HWI-ST960:105:D10GVACXX:2:1101:13873:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGGGGGTCCCAGTTCCGAACCC + HHHFFFFFFFEECCCFFDFFGHHHHJJJJJIIJ @HWI-ST960:105:D10GVACXX:2:1101:13832:2175 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTTGTGCCTTTTTCTCTTCT + HJJJJJIJJJJJC@CFFFFFHHHHHJJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13756:2181 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGATCACAGTCGGCTTACCCGGGGAC + DCFFEEEEDDDD@CCFFFFFHHHHHJJIIIJJJ @HWI-ST960:105:D10GVACXX:2:1101:13888:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTGAGAGATTTCGTAAAAAAC + IJJJJJJJHHHHCCCFFFFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13863:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTGGTTGGTGTAAAAAAAA + HHHFFFFFEEEEBCCFFDFFHDFFHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13978:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTTGACTCTGTAGCTTTACTT + HHIHJJIJIIJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13770:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCCAACATATGTTTCATAATGT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13874:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCATAAAAGTTGTCGTAGCATAA + IJJIJJJJJJJH@CCFFFFDHHHHHJJJJJJHH @HWI-ST960:105:D10GVACXX:2:1101:13985:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCTCTTGACTTGCCTCCTTACC + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:13941:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCTATTTATATATTTGATGTTT + JJJJJJJHIJJJCCCFFFFFHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:13963:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTCTGTCTATTTCGTTAAATC + JJJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:13752:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTTTGTCAATTGTCATATTTGC + JJJIIJJJJJJJCCCFFFFFHHHGHJJJJJJHI @HWI-ST960:105:D10GVACXX:2:1101:13859:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTCTGTTTCAATGTCCCTTGC + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ<4 @HWI-ST960:105:D10GVACXX:2:1101:13939:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGAGTCAAGACTCAAGACTAT + IJJJJJJJJJJJBCCFDFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14150:2157 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCACNGTTGTAGTCTCTGTGTAT + HIJIJJJJJJJJCC#4ADDFHHHHHJJJHHHHJ @HWI-ST960:105:D10GVACXX:2:1101:14171:2160 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCGNATGAACTCTGGTTTAGTT + HHJHJJJJIJJICC#4ADFFHHHHHJGHJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:14041:2163 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTANATATGTAGTCTTATGTCT + IJJHJJJJJJJJCC#4ADFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14084:2164 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGATCTCNGATGATGATCAAATCAT + HFHIFIJIIJIJCC#4ADDFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14180:2173 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCACAACAGCATATTTATAAA + FBF@GGIIGGHI@@@FFFFDHHBDHIJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14103:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAACAAAAGTGGCTGTAGTTT + JJJJJJJJJJJJBCCFFFFFFHHHHJIJJGJJ @HWI-ST960:105:D10GVACXX:2:1101:14196:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTAGGTGTTACTGTGGATTTC + G4BFFHEHIHGE:==DD2BDHHBHDIEE@DGHE @HWI-ST960:105:D10GVACXX:2:1101:14128:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTAATGTAGTAGCAACTCTT + JIJJJJJJJJJJCBCFFFFFGHHHGJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14033:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTGGTAACTGGACTCTGAT + HGIJJJJIJJJJC@CFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14074:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTAATACACTTTCCCTTACAT + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14019:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCTCTCTGTGATTCTCTTTTTA + HDGFHJIGJIGICCCFFFFFHHHHHIJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:14232:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAAGCTGGAAACTTTGAGCTT + IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14143:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTTGTGGCACACTAAGCTG + JGJJJJJJJJJJ@CCFFFFFHHHHHJJJJJI3 @HWI-ST960:105:D10GVACXX:2:1101:14121:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTCTAGTAGCATGTGAATTTA + IIIIIIIIIIII@??DDAD;?DHD?DDHGEGC @HWI-ST960:105:D10GVACXX:2:1101:14168:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATTCTATCGGATTCTCAAC + IGJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14102:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTGTATTTGATCTACATTGTAT + HGHGIJIJIIGIBCBFFFFFGHHGHJIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTCCCGAACTCTACGTAGAAAT + IJJJJJJGJJJHCCCFFFFFHHHHHJHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14209:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTACTCAACACTCTCTTCTT + IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14087:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGAGTTCTTAGCCATTGCAT + IGIJJJJJJJJJCCCFDFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14127:2230 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCACTCTGGATTCAATTTGGAT + JJJGIJJJJJIJ@CCFFFFDHHHHHJJIIJJI @HWI-ST960:105:D10GVACXX:2:1101:14273:2157 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTNCTCGTCGCTTGTGGCTC + H@EHIHHHHHHHCC#4ADFDHHHHHJFHIHIH @HWI-ST960:105:D10GVACXX:2:1101:14385:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCGNGACAAAAGAACTGGACTC + IJJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14449:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTCNCTGTCACAATGGTTAAAC + IJJJJJJJJIJJCC#4ADDDHFHHHJIGIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14408:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTNTGTTTTTCCCAAAATAC + HHJJJJJJJJJJCC#4ABDFHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:14427:2163 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTNACAGAAGATAGAGAGCAC + HJJJJIJJJJJJCC#4ADFFGHHHHJJIIJJGI @HWI-ST960:105:D10GVACXX:2:1101:14472:2172 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATAACGATCCTCTGTGTCTCTCTCGATCGA + HHJJJIJJJJJHCCCFFFFFHHHHHJJJJJJ33 @HWI-ST960:105:D10GVACXX:2:1101:14402:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAATAAAGTGGTCTAGTGGTT + IJJJJJJJJJJJCCCFFFFDHHHHHJIEGIHG @HWI-ST960:105:D10GVACXX:2:1101:14443:2185 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTTTTACTGTCCTCTGATCAG + JJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJ3 @HWI-ST960:105:D10GVACXX:2:1101:14420:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTATGTATATATAAGAGTCAT + IJJHJJJJJJJJCBCFFDFFGHHHHJJJJHHGJ @HWI-ST960:105:D10GVACXX:2:1101:14467:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGAAACTGTACTTGAGATTA + JJJJJJJJJJJJCCCFFFFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14311:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTCTTTATGGCTCTAGTACAA + JIJJJJJIJJJJCCCFFFFFHHHHHJJJIIJJJ @HWI-ST960:105:D10GVACXX:2:1101:14442:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAAAAATGTCGTTGTAGTATAG + JJJJJJJJJJJJCCCFFFFEHHHHHHJJIIJGI @HWI-ST960:105:D10GVACXX:2:1101:14388:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAATTCCAGTTGATTGAGGTC + ICHIHIFHIJJJCCCFFFFFHHHHHJGHJJII @HWI-ST960:105:D10GVACXX:2:1101:14404:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGTTGTTGGCTATGATGTTAT + HIIJIJJJJJJJCCBFFFFFHHHHHIIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14361:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAAATTATGATGGAAGATTTGT + HHJJJIJJJJJJCCCFFFFFHHHHGJJHJJJ34 @HWI-ST960:105:D10GVACXX:2:1101:14303:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCACATTTAGGCTCAGTGGGA + JIJJJJJJJIJJCCCFFFFFHHHHHJGHIIG @HWI-ST960:105:D10GVACXX:2:1101:14342:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGCTCTTCAACCTTAGAAGA + IGJJJJJJJJJICCCFFFFFHHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14263:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTACTTTCTCGTGCTAACTC + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14722:2164 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTNGTTGGCCTTAAAAAAAA + EEHHEHFFFFFECC#4ADFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14632:2164 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGNTGATTCTCCTTAGATCTG + FHIIJJJJIIJICC#4ADDFHHHGHJJJJJJGI @HWI-ST960:105:D10GVACXX:2:1101:14512:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGCAATCCCTCTGTTTCCTAA + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14677:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTGACAGAAGATAGAGAGCAC + IIJJJJJJJJJJCCCFFFFFHHHHHJJJJIIGJ @HWI-ST960:105:D10GVACXX:2:1101:14738:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAATGTTCATGTCTAAATTCG + HHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ3 @HWI-ST960:105:D10GVACXX:2:1101:14684:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAAGCCGGAGACAGGAGAGGTG + HHHHFFFFEEEECCCFFFFFHHHHHJJJJJJ*? @HWI-ST960:105:D10GVACXX:2:1101:14526:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCACATAGACTAATCTTATAAT + JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14580:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAAATAAGGTATCAGGTTTTA + IIJIJJJJJJJJCCCFFFFFFFHHHJJEHIJJ @HWI-ST960:105:D10GVACXX:2:1101:14592:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTTATAGGGAGAAGAAGAGGC + HDHIJIJJJJHHCCCFFFFFHHHGHJJJIJJ34 @HWI-ST960:105:D10GVACXX:2:1101:14659:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATTGGTGCCTGTAGGTCAG + IHJJJJJIJJJJCCCFFFFFHHHHHJJJFHI3 @HWI-ST960:105:D10GVACXX:2:1101:14548:2237 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCAATTTTATGTCGTTTCTTTG + JJJIIJJJJJJJCCCFFFFFHHHHHIJJJJJ< @HWI-ST960:105:D10GVACXX:2:1101:14792:2167 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCTANGGTTTGGCTGTTAACAC + FBGE>FHIJJHHB@#4ABDFHHHHHIJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14962:2168 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATCCACACTAAGTCCAAGC + HIJJJJJJJJJJCCCFFFFFHHHHHHIJIJJG @HWI-ST960:105:D10GVACXX:2:1101:14851:2171 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTATTTGTAGCAATTCTGTTTT + IJJJJJJJIIJICCCFFFFFHHHHHJJIIFHHJ @HWI-ST960:105:D10GVACXX:2:1101:14982:2172 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCGTAATCTGGGATGAACTCACT + JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14927:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATTCTTGTTTAGAAGCAAGAA + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:14906:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGCCAACTCTGTTTCTTCTTCT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJIJIJ @HWI-ST960:105:D10GVACXX:2:1101:14858:2195 1:N:0: bcd:RPI3 seq:CACTTAGGCATC CACTTAGGCATCATTCGTTTCAATGTCAATCTC + IIIHGIHGIJJJ@BCFFDEFHHHHHIJJIJJII @HWI-ST960:105:D10GVACXX:2:1101:14936:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGCCAATGTTGTAGAACTAT + HIIIIIIIIIII@@CFFDFFHDAFFBHIG@H@ @HWI-ST960:105:D10GVACXX:2:1101:14780:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTTGTGAATCCTTTTCCATT + IGJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14808:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATGAAGAGGCTGTTTCTAC + IGIJJJJJJJJJCCCFFFFFGHHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14828:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATGTATGTTGTTATTTGATAA + HGIGIGIJHIJI@CCDFFFFHHHHHJJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14929:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAACACTCTTATCAAAAAAAA + IJHHHHFFFFEECCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:14844:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCATACATCTTTGCAGAACTCAT + HIIC=CGCFGIH@C@FFFDFHGFDFD @HWI-ST960:105:D10GVACXX:2:1101:14761:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATTTGTAGTCGTAAATATCT + IHJJIJJJJIJJCCCFFFFFHHHHHJIJIIII @HWI-ST960:105:D10GVACXX:2:1101:15012:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAANTTCTCCCATCAGTTACAA + IIJJJJJJJJJJC@#4ADDFHHFHHJJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:15055:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAGNAACTGTATCTATGTCGT + JJJJJJJJJJJJCC#4ADFFHHGHHJJJIIJG @HWI-ST960:105:D10GVACXX:2:1101:15030:2168 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTCTGTTACACGCCGAGATC + JJJHHHFFFFFECCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15079:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTCAGGGCAAGCACAACATAT + JJJJJJJJJJJJCCCFFFFFHHGHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15143:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCATCTTTTTCATCCCAATCTGT + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ<3 @HWI-ST960:105:D10GVACXX:2:1101:15178:2193 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAGTGATGAACCTTTTGAACC + IJJJJIJJJJJJCC@FFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15053:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATCCAGTCTCATCGCTGTTG + IJJJJJJJJJJJCCCFFFFFHHHHHJIJJJJEI @HWI-ST960:105:D10GVACXX:2:1101:15025:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCGTATGTAAAGGTTTACTCTTT + JJJJJJJHIJJJCCCFFFFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15186:2216 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCAGAGCAAGTCGAAATCTGTT + JJJJGJJJJJJJCCCFFFFFHHHHHJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:15065:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTGTGCTGGGAACTATTTGAC + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:15143:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATGAAAACTTCTTGAGTTAT + IIJJJIJIJJJJCCCFFFFFHHHHHJJJIIJJ @HWI-ST960:105:D10GVACXX:2:1101:15008:2227 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTTTCTTGGGACTTGATTTTT + IGIHIJHGHHFF#CCFFFFFHFHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15207:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTAGTGTGTAATGTTATTGG + IIJIJJJJJJJJBCCFFEFDHHHHHJHJJJJ34 @HWI-ST960:105:D10GVACXX:2:1101:15000:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTTGGTCATGTTTGCTATTTG + FFF;FF@G3=DC@CCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15342:2165 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCCGNATCTGGATTTAAGATAA + IGIIIJJJJJJJCC#4ADFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15274:2198 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCATCTGTCTAAAGTTTGTTCT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15308:2216 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGTAATTTAGCATGTTGCAAA + IJJIIJJJIIJICCBDFFFFHHHHHJJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:15475:2222 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTCTGTAGTTGTATTTCAAC + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15291:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATGTTGTTAGCTATCACT + IHJJJJJJJJJJC@CFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15347:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTGAACTCTGACCAATGAACTT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15331:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTGTTATATATTACTGACTAC + HJJJJIGIJJJJCCCFFFFFGHHHHJJJJJJDI @HWI-ST960:105:D10GVACXX:2:1101:15450:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTGTTTTGTCCCTTTGTATTT + JJJJJJJJJJJJCCBFFFFFHHHHHJJHIJJJ @HWI-ST960:105:D10GVACXX:2:1101:15610:2159 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGNTCTGATTTCAATTTTTGC + JJJJJJJJJIJJCC#4ADFFHHHHHJJJJJI33 @HWI-ST960:105:D10GVACXX:2:1101:15730:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAGNCTGCTACAACAAAAAAAA + HHH>DFDDCEEDCC#4ADFFHHHHHJJJJJJIH @HWI-ST960:105:D10GVACXX:2:1101:15650:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTNTTGGCAGCGTATCTTTTC + HIJJJJJJJJHHCC#4ADFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15745:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNATGTCATTAATGAAAACT + HIJJJJJJJJJJ@@#4ADDFGHHHFJJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:15691:2179 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTACTAGTCTCGTATTAACTA + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:15591:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTTTGCTTATGTGCCCGTTTT + IIJJJJJJHHHHCCCFFFFFHHHGHJJJJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:15612:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATATCCTATGTCTAAAAAAA + IIJIJJJHHHHHCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15528:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCATTTCGGATCTTGGCTACTAA + IJJIJJJJHHHHCCCFFFFFHHHHHJIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15503:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAATCTAAAGGGATTTGGTGT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJHII @HWI-ST960:105:D10GVACXX:2:1101:15541:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC CAAACTTGAATCGTCTGTAGCTCTAGACCATTC + IIIIJJGIGIJJ@CCFFDEFHHFHHJIJGGIJH @HWI-ST960:105:D10GVACXX:2:1101:15700:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTAAATTCTCTTCCTTTGGT + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJG @HWI-ST960:105:D10GVACXX:2:1101:15649:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTAATGTGATGGTTTCTTCAA + IIJJJJJJJJJJCCCFFDFFHHHFHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15573:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATAGCTAGTCATAACTCTTT + IJIJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15731:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAATATGTTTCGTAGAACTAT + JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15639:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCTTTTACGGAGTACAAGAGAT + JJJJJJJJJJJJCCCFFFFFHHHFHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15900:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGCNAGATGATGGTCATTATAA + IJJJJJJJJJJJCC#4ADFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:15963:2161 1:N:0: bcd:RPI1 seq:CACATCACGATC CACATCACGATCATNTGTAAATATACCACGAAT + C=GI@=CHC7=E@@#4==BDA?DFHG@ @HWI-ST960:105:D10GVACXX:2:1101:16438:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATGTTCGGTTGTGGGATTCT + HIJJJJJJHHHH@BCDFFFFHHHHHJJGJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16355:2177 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTTGTTAGACTCTTCGATTT + HGHJJIJJIJIJCCCFFEFFHHHHHJJJJJJGJ @HWI-ST960:105:D10GVACXX:2:1101:16306:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTACCTACTCGTCGTACATTTT + HJJJJJJJHHHHCCCFFFFFHHHHHIJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16427:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGTTGATTTTAATGGTTACTGT + BFHIJGHIEHII@CCFFFFFHHHHHJFHGHIIJ @HWI-ST960:105:D10GVACXX:2:1101:16368:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATAAAAACTCTGAATTTAAT + IJJJJIJJIJJJCCCFFFFFHHHHHJJJJIJC @HWI-ST960:105:D10GVACXX:2:1101:16496:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTTCTGTTGAACCTCTTG + HHJIIIIJJJIJCCCFFFFFHHHHHJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16268:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTCAAACCATTGAGACAGCTT + HIJJJJJIJJJJCC@FFFFFHHHHHJJJJJJGI @HWI-ST960:105:D10GVACXX:2:1101:16478:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCCTGTGAAACTGCGAATGGCT + F=FHIHJGIJJHCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16378:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTACGTTATTTAAAATCCTC + IJIJJJJIJJIJCBBFFDFFHHHHHIJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16273:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGTTATGTGACTGGAGAGA + IIJJJIJJJJJJCCCFFFFEHHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16350:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTGTGGCTCAGAACCACCAC + IIJHIJJJJHHHCCCDFFFFHHHHGJJJIJII @HWI-ST960:105:D10GVACXX:2:1101:16328:2230 1:N:0: bcd:RPI4 seq:CACTGACCAATC CACTGACCAATCACTGATCGCGTCGTGTTAC + HIJJJHHHHHFF@BCFFFFFGHHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16408:2232 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTTCGAACAATGAACAATTGC + HIJJJJJJIJJHCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16369:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTACATTGTGAAATGATATTTC + HGEGGIJGIJJJ@CCFFFFBHHHHFGIIJJJJI @HWI-ST960:105:D10GVACXX:2:1101:16305:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCAAACCTGTATCTGTGTAACT + IIJGIJJJIJJJCCCFFFFFHHHGHGJIGHIIJ @HWI-ST960:105:D10GVACXX:2:1101:16684:2159 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTNTTCGGATTTGAACAGA + JIIJJIJJJJIJCC#4ADFFGGHHHJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16513:2160 1:N:0: bcd:RPI5 seq:CACACAGTGATC CACACAGTGATCTGNTATGTTGGTTAAGACTTT + JIIIIII@C=DH@C#4ADDDFHHFHIJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:16553:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCACNGTTTTGCTAAAATATTC + HAHGIJJIJJIJCC#4ADDFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16647:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTAATTGAATATCTTCAATGT + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16734:2178 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTACGAATTCTAAATTTTAT + HIJIJJJJJJJJBBBDFFDDHHHHHJJJJIIJ @HWI-ST960:105:D10GVACXX:2:1101:16682:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTATCAATAAGCGGAGGAAAAG + HIIGHGGHHHFF@@@FFFFFHHAFFHDDHIIII @HWI-ST960:105:D10GVACXX:2:1101:16516:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGAGAGTTCGAATCTGTCAGGC + GIJJJJJJJJJJCCCFFEFFHHHHHJJGIJJIJ @HWI-ST960:105:D10GVACXX:2:1101:16583:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATCGGCGCTTGTTCACCTCTC + HIHHHHHFFFFFCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16633:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCATTGTATTTTAACAGCACTC + JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16696:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTATGTAATGTAGTCTTTTAT + GGHIIIJJIIJJ@C@DDDDFHFFHDBGIIIIH @HWI-ST960:105:D10GVACXX:2:1101:16666:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCTTAACACTTGGTTCCGTTTC + IJJJJJJJJJIJCCCFFFFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16730:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCCTATAAATCGTCTCATGAA + JJJGIJJJJJJJCCCFFFFFHHHHHJJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:16561:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATAACCCTTTCCAGGCCATGT + CDHIGHIIIGCD@@CFDEFFHHDHHGFBHEGGJ @HWI-ST960:105:D10GVACXX:2:1101:16708:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCACCATTGTCTGAATAAAAAG + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17000:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTNATCCTCGTTATATTTGT + FFFIIIIIIIFI==#4=2ADFAFFF@FIIE@C @HWI-ST960:105:D10GVACXX:2:1101:16900:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGANCAAACCGACACTCGGGAT + HHHHFFFFFFEECC#4ADFFHHHHHJJJIJJHI @HWI-ST960:105:D10GVACXX:2:1101:16800:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATNTATTTGGGGTTATTTGCA + HIJJJJJJJJJHCC#4ADDFGHHHFHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16874:2165 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCTTNGTTGAACGACAAAATAA + GHIHEDEHHGFF@C#4=BBDHFHHGGIGJEGG @HWI-ST960:105:D10GVACXX:2:1101:16973:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCACNGTGTTGGCGTTTTATCTG + IJIIJJIGIHHHCC#4ADDDHHHHHJJJIJJJI @HWI-ST960:105:D10GVACXX:2:1101:16783:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGGNTGTGCAGACTAAGGAGC + FFFIIIFIIIII@@#4=DDDFFFFFIIIIIII @HWI-ST960:105:D10GVACXX:2:1101:16847:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCGATGTCGGCTCTTCCTATCAT + GIJJJJJJJJJJCCCFDFFFHHHHHJGIGIIIJ @HWI-ST960:105:D10GVACXX:2:1101:16809:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCACATCCTCATAATCACTTTC + FDHJJEFIGIIJCCCFFFFFHHHHHIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16946:2180 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTCTTTTGTCGGCGTTAGGT + HHHHFFFFEEEECBCFFFFFHHHHHJHJJJJH @HWI-ST960:105:D10GVACXX:2:1101:16831:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTATGTTATGGATTCAAAAAAA + HIJJJJJHHHHH@CCFFFFFHHFHHJIJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16770:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTCAGCCCTTTGTCGCTAAGA + HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16858:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAATTTTTAGTGACCCTTTTA + HIJJJIJJJJJJ@@@FFFFFHFFHHJIJJJJI @HWI-ST960:105:D10GVACXX:2:1101:16876:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTATGTTCTCTGTTATTCTC + IIJJJJJJJJJJCBCFFFFFHHHHHJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16983:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCTTTGTGGGTTGAGTTGTCT + HIJIJJJJIJHHBCCFFDFFHHHHHJHIJJIJ @HWI-ST960:105:D10GVACXX:2:1101:16842:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTATGAAATCGACCATGACA + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16962:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTCATGCTGTTTTCCAACAGC + IJJEIIJJJIGH@CCFFFFFHHHHHJJIJJJIJ @HWI-ST960:105:D10GVACXX:2:1101:16751:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTACTGTTTTCTGTTTTCTT + JJJJJJJJJJJJC@BFFFFFHHHHHHIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16898:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCAACCCCCGAACTATATCCTC + HIJJJJHHHHHFCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:16969:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCATTATCTTGTAGAATGTTCA + HGIJJJJJJJJJCCCFFFFFHHHHHJJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:16781:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTTCTCCTCTCGTCCATAAAT + IJJJJJJJJJJHCCCFFFFFHHHHHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17176:2160 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGCNAGATGATGGTCATTATAA + GIJIJJJJJIJJ@@#4ADDFGHHHFGIJJIJJJ @HWI-ST960:105:D10GVACXX:2:1101:17068:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTNCACAAGAAAATCAAATAA + HIJJJJJJJJJJCC#4ADFFHGHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17154:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTNGTGGATGATGAAGAGTT + HII;@HGGHIII@@#44ADDFHHBFGEGGICF @HWI-ST960:105:D10GVACXX:2:1101:17222:2169 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTGGATCCTGTTTTGGATTGT + IIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17028:2180 1:N:0: bcd:RPI6 seq:CACGCCAATATC CACGCCAATATCCTATTTACTATTTGAAAAAGC + IJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17127:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCAATTGGACTGTTTAACGTTT + JGIJJJJJJJJJCCCFFFFFHHHHHJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:17143:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCAAATTTCTATATATTGTTTT + JJJGGJIIGJJJ@@;DDFFFHGHHGJJJFHIJ @HWI-ST960:105:D10GVACXX:2:1101:17161:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCTTCTGGACATTAGCCATTAGT + HIJJJJJJJJJJCCCFFFFFHHHGHIJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17133:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCTGCCTTTTCCTTCTTGTCGG + JJJJJJJJJJJJ@@CFFFFFHHHHHJIJIIJJ @HWI-ST960:105:D10GVACXX:2:1101:17121:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGGCACTTCTGTTCTGATCCT + JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17033:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCACTAGACAAACTCTCAAGA + IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJI @HWI-ST960:105:D10GVACXX:2:1101:17178:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGTTTGTAGTCATAATTTAGT + IJJJJJJJIJJJCBCFFFFFHHHHHJIJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17141:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCGTATGTTTCACTCTGTAACT + JJJJJJIJJJJJCCCFFDFFHHHHHJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17119:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCGAGACCAGATGTGCGATGTTT + IJJJJJJIJJJHCCCFFFFFHHHHHJJJJJIJJ @HWI-ST960:105:D10GVACXX:2:1101:17246:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC CACACTTGAATCATTTGGTTAGGTCCTTTGTTC + JJJJJJJJJJJJCCCFFFFFHHHFHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17011:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTTTTGAGGTTTTAAGATGTT + HIJJJJJJJJJJBCCFFFFFFHHHHJJIJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17270:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC CACGATCAGATCCCNCTCTTTCAATGCAAATTT + IJJGJJJJJJJJCC#4ADDFHHHHHJJJJJJJJ @HWI-ST960:105:D10GVACXX:2:1101:17469:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC CACCAGATCATCTGTGTTGGTGAAGGAAGGAAC + GHI@FFG;CHIH@@+ADDDDAFHDFEG@?A?FB libqes-0.1.21/test/data/test.fastq.bz2000066400000000000000000000425461263611052100174650ustar00rootroot00000000000000BZh91AY&SY þO`߀ÐHûÿÿÿñ]À(`qÿ}£H¾ñSæ4|>€ é•ôЛM£[M6  JRFÜîÇÐú(J7·¯^Ö]™Ûï½Åë G`2ô T<=rûÎâäãU÷w£|w0´ï¹{ÁïÙgÓèÔ© {=ðô¾šÓmWq»ÉÏXÒöûµÉIÝÜî¼y“TÒï@Ðm²Ð>÷Ц©¶Ëï:#'ßeÙÔeškfµ™ðúÇ;ÝÛKl®í¹Û»U§FO±@h€P4õC]PÕ*Š  ¢€§ˆ "M )²iOSCOÒšhziIQF Òzƒ dbbd10Jy)*¨ýPƨޣM ¦€Ñ€&™„§’•4¥1= H„!4Ñ MJ~šSÐFIÒ4Á&ŠB"%?Tôôšƒ@ÐЀÿ_Ø€ ²"°GöþÖPQd+?§çù;Õgôþ’‚}õYä§éhÜ+4!'^+çG¡w\â1.wT^D9«DjtÛy.õßmSÓX ùç¤ö„™#îC2û¡Dðáå[F–ÛI™R¡·Jùv•A8C¥EyºòʈÛXÚJží‚$$PzUŠDS¸q$+åQQè’L‚Ï)WËÃÁN§\¡œ—¶œœÆ½LSf 2̾Z@%'€Yäég†äXx<éíç^5!-,q O®ÚïÎú}¶›îþZˆùúqyùî¸Ùí¢do¬_Y¹r7AáLã9Œå‘¥~˜ýŸç—ã}î}[z~Ûq?FPú†ß‹í,9º[Ì+SŠLÌÜR?hîÇåM~öæÂ÷í+—“Íû=­:ï;£m¦9j‹åÑçØ®úc×O òú©yT ù“MŠOY™•‡ ~r7H¾sñ6FÉMò¿O&¹›ðù#á}qUòÈ6n·’>ÛÞgêï«Ú¶*‡¯Ã÷ÞøyëПX¤öØ›5lH³- gˆMÎÑ…¬s$=ùÓÞÞ¡Ù¡”ݺÂM-‘Âö3zr'4¶J7 4! 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4˸ޫÅÎ'-ŸXcܤ­>ILmê.f:Às$Ñ\@ìœÂnbÐcVAEUàyúÁãÑD«µ¸5®5¯õXKö¬öªßHâ!_S!£™§Mÿ¦?^|ÉžÕ7B ùWË6„©_þ&÷ŠS=rÕÕ)àìg]²cˆÐ¢ýýÂê. * ýý0˜:ê6A‘” Uo$÷9h…zË 3R³>M+±j‹Ê7·)˜#Þ§ˆ'‘ݵ'jŸ7$ ¦’õ±ýÌèÞÂSRŽvC¼c!Ȇ½†7Æ q+h»\ðT‚ÉÖ³~ãà ©èƒÅE5Œ¢¤ËnÐ9t\CÓ¡³Õã¶@¢;VW¾}8ëXvÕ+ r¿…›‰ëT-½A±ìYØ)r†%pŽYÐÌòì[Ýì5I#ü†øònÑšWŠ€M[ß!=$ëSe>ó`mˆð8-iVy@ü: šg¦³âÕK¸BuIúxf~gŽûãÃ=êÙNRô[Õ´M‚Ê E¯LΓ {ñ iYò޵ ™ ®ùa(þØ”¼'Hß×7¾TY½€¨¡–wNuŽÌ’2 úNoP¬ÂÌW¸isP›r ’øžú Z‰˜r a\°øî68žÞ«y²5*½ 3a‹ Tb¡7\æ_Ï Ù´]".Ÿu#fµ€“¥Î2/dpú¯5ã*6Õhg^Ü-«oÐO‰œbA07VO)¢>Ì}ehÇÒø¼hXœßFu(å¯=‡¨þZ3§F¬Žµ˜anŒlý®kîDÞóù \ƒž‹MÊ$öTÞ™¤°'}Φ] ¾ãø0QïÕÎ.Q¬B35æÉ4C=qÊÙ›ˆ¾.¢ìTEST Comment 1 AGCT libqes-0.1.21/test/data/truth/qes_seq_print.fq000066400000000000000000000000341263611052100213060ustar00rootroot00000000000000@TEST Comment 1 AGCT + IIII libqes-0.1.21/test/helpers.c000066400000000000000000000140221263611052100156330ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: helpers.c * * Description: Helpers for tests * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "helpers.h" /* This is how we name out output files, n_writables is the num of writable files we've made. */ static int n_writables = 0; /* This holds the prefix. It is set (via extern) in test.c's main func. */ char *data_prefix = NULL; /*=== FUNCTION ============================================================* Name: find_data_file Parameters: filepath: the file, under ./data, to find Description: Finds the full path to ``filepath`` Returns: A ``char *`` on the heap that contains a valid path to the file ``filepath``, or NULL on error; *===========================================================================*/ char * find_data_file(const char * filepath) { size_t buflen = 1<<12; size_t len = 0; char buf[buflen]; /* Bail out if we can't get the data_prefix. */ if (data_prefix == NULL) { return NULL; } len = snprintf(buf, buflen, "%s/data/%s", data_prefix, filepath); /* File name is too long, return NULL */ if (len >= buflen) { return NULL; } /* Null terminate AFTER making sure len < buflen */ buf[len] = '\0'; /* Check we can access the file. If so, strdup & return */ if (access(buf, F_OK) == 0) { char *ret = malloc(buflen + 1); assert(ret); return strncpy(ret, buf, buflen); } /* If we get to here, something's gone wrong. */ return NULL; } /*=== FUNCTION ============================================================* Name: get_writable_file Parameters: void Description: Gets a temporary file which can be written to, under the data directory. Returns: A ``char *`` on the heap that contains a valid path to a file writable file, or NULL on error; *===========================================================================*/ char * get_writable_file(void) { size_t buflen = 1<<12; size_t len = 0; char buf[buflen]; char *ret = NULL; /* Bail out if we can't get the data_prefix. */ if (data_prefix == NULL) { return NULL; } len = snprintf(buf, buflen, "%s/data/%05d", data_prefix, n_writables++); /* File name is too long, return NULL */ if (len >= buflen) { return NULL; } /* Null terminate AFTER making sure len < buflen */ buf[len] = '\0'; /* Check we can access the file. If so, strdup & return */ ret = malloc(buflen + 1); assert(ret); return strncpy(ret, buf, buflen); } /*=== FUNCTION ============================================================* Name: clean_writable_file Parameters: char *: filename Description: Unlink ``file`` and free the memory holding the path. Returns: void *===========================================================================*/ void clean_writable_file(char *filepath) { if (filepath != NULL) { remove(filepath); free(filepath); } } /*=== FUNCTION ============================================================* Name: crc32_file Parameters: char *: filename Description: Calculate (using zlib) crc32 checksum. Returns: const char *: The crc32 sum, or NULL on error. *===========================================================================*/ char * crc32_file(const char *filepath) { FILE *fp = NULL; size_t buflen = 1<<10; size_t len = 0; char buffer[buflen]; uint32_t crc = 0; char crcbuf[9]; /* Open file */ fp = fopen(filepath, "rb"); if (fp == NULL) { return NULL; } while (!feof(fp)) { len = fread(buffer, 1, buflen, fp); crc = crc32_update(crc, buffer, len); } len = snprintf(crcbuf, 9, "%08x", crc); crcbuf[len] = '\0'; fclose(fp); return strdup(crcbuf); } int filecmp(const char *file1, const char *file2) { /* returns: -1 on error, 0 if identical, 1 if not */ FILE *fp1 = NULL; FILE *fp2 = NULL; unsigned char *buff1 = NULL; unsigned char *buff2 = NULL; const size_t buff_size = 65535; int retval = 1; if (file1 == NULL || file2 == NULL) return -1; fp1 = fopen(file1, "r"); fp2 = fopen(file2, "r"); buff1 = malloc(buff_size); buff2 = malloc(buff_size); if (fp1 == NULL || fp2 == NULL || buff1 == NULL || buff2 == NULL) { retval = -1; goto exit; } while (!feof(fp1) && !feof(fp2)) { size_t bytes_read = 0; size_t res1 = 0; size_t res2 = 0; res1 = fread(buff1, 1, buff_size, fp1); res2 = fread(buff2, 1, buff_size, fp2); if (ferror(fp1) != 0 || ferror(fp2) != 0) { retval = -1; goto exit; } if (res1 != res2) { retval = 1; goto exit; } if (res1 == 0 && res2 == 0) { break; } bytes_read += res1; if (memcmp(buff1, buff2, res1) == 0) retval = 0; } exit: if (buff1 != NULL) free(buff1); if (fp1 != NULL) fclose(fp1); if (buff2 != NULL) free(buff2); if (fp2 != NULL) fclose(fp2); return retval; } libqes-0.1.21/test/helpers.h000066400000000000000000000031001263611052100156330ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: helpers.h * * Description: Helpers for tests * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef HELPERS_H #define HELPERS_H #include #include #include #include #include #include #include #include #include #include #ifndef _WIN32 # include #endif #include extern char *data_prefix; char *find_data_file(const char * filepath); char *get_writable_file(void); void clean_writable_file(char *filepath); char *crc32_file(const char *filepath); int filecmp(const char *file1, const char *file2); #endif /* HELPERS_H */ libqes-0.1.21/test/kseq.h000066400000000000000000000211531263611052100151440ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2009, 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Last Modified: 05MAR2012 */ #ifndef AC_KSEQ_H #define AC_KSEQ_H #include #include #include #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r #define KS_SEP_TAB 1 // isspace() && !' ' #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) #define KS_SEP_MAX 2 #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ unsigned char *buf; \ int begin, end, is_eof; \ type_t f; \ } kstream_t; #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(type_t, __bufsize) \ static inline kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ ks->buf = (unsigned char*)malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ { \ if (ks) { \ free(ks->buf); \ free(ks); \ } \ } #define __KS_GETC(__read, __bufsize) \ static inline int ks_getc(kstream_t *ks) \ { \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) return -1; \ } \ return (int)ks->buf[ks->begin++]; \ } #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #define __KS_GETUNTIL(__read, __bufsize) \ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ { \ if (dret) *dret = 0; \ str->l = append? str->l : 0; \ if (ks->begin >= ks->end && ks->is_eof) return -1; \ for (;;) { \ int i; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) break; \ } else break; \ } \ if (delimiter == KS_SEP_LINE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == '\n') break; \ } else if (delimiter > KS_SEP_MAX) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == delimiter) break; \ } else if (delimiter == KS_SEP_SPACE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } else if (delimiter == KS_SEP_TAB) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (char*)realloc(str->s, str->m); \ } \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ if (str->s == 0) { \ str->m = 1; \ str->s = (char*)calloc(1, 1); \ } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ str->s[str->l] = '\0'; \ return str->l; \ } \ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { return ks_getuntil2(ks, delimiter, str, dret, 0); } #define KSTREAM_INIT(type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(type_t, __bufsize) \ __KS_GETC(__read, __bufsize) \ __KS_GETUNTIL(__read, __bufsize) #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) #define __KSEQ_BASIC(SCOPE, type_t) \ SCOPE kseq_t *kseq_init(type_t fd) \ { \ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ s->f = ks_init(fd); \ return s; \ } \ SCOPE void kseq_destroy(kseq_t *ks) \ { \ if (!ks) return; \ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ ks_destroy(ks->f); \ free(ks); \ } /* Return value: >=0 length of the sequence (normal) -1 end-of-file -2 truncated quality string */ #define __KSEQ_READ(SCOPE) \ SCOPE int kseq_read(kseq_t *seq) \ { \ int c; \ kstream_t *ks = seq->f; \ if (seq->last_char == 0) { /* then jump to the next header line */ \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ if (c == -1) return -1; /* end of file */ \ seq->last_char = c; \ } /* else: the first header char has been read in the previous call */ \ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \ if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \ seq->seq.m = 256; \ seq->seq.s = (char*)malloc(seq->seq.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ if (c == '\n') continue; /* skip empty lines */ \ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \ ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \ } \ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \ seq->seq.m = seq->seq.l + 2; \ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ } \ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ if (c != '+') return seq->seq.l; /* FASTA */ \ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \ seq->qual.m = seq->seq.m; \ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ if (c == -1) return -2; /* error: no quality string */ \ while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ seq->last_char = 0; /* we have not come to the next header line */ \ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \ return seq->seq.l; \ } #define __KSEQ_TYPE(type_t) \ typedef struct { \ kstring_t name, comment, seq, qual; \ int last_char; \ kstream_t *f; \ } kseq_t; #define KSEQ_INIT2(SCOPE, type_t, __read) \ KSTREAM_INIT(type_t, __read, 16384) \ __KSEQ_TYPE(type_t) \ __KSEQ_BASIC(SCOPE, type_t) \ __KSEQ_READ(SCOPE) #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) #define KSEQ_DECLARE(type_t) \ __KS_TYPE(type_t) \ __KSEQ_TYPE(type_t) \ extern kseq_t *kseq_init(type_t fd); \ void kseq_destroy(kseq_t *ks); \ int kseq_read(kseq_t *seq); #endif libqes-0.1.21/test/logdemo.c000066400000000000000000000034211263611052100156200ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: logdemo.c * Description: Demontrate libqes logging * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include int main (int argc, char *argv[]) { struct qes_logger *logger = qes_logger_create(); (void) argc; (void) argv; qes_logger_init(logger, "Test Logger", QES_LOG_DEBUG); qes_logger_add_destination_formatted(logger, stdout, QES_LOG_DEBUG, &qes_log_formatter_pretty); qes_log_message_debug(logger, "Debug message, nice and quiet\n"); qes_log_message_info(logger, "Informative message, clearer\n"); qes_log_message_warning(logger, "Warning message, pay attention!\n"); qes_log_message_error(logger, "Error message, something's gone wrong\n"); qes_log_message_fatal(logger, "Fatal message, I'm leaving now\n"); qes_logger_destroy(logger); return EXIT_SUCCESS; } libqes-0.1.21/test/test.c000066400000000000000000000045421263611052100151560ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test.c * * Description: Tests for libqes * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" struct testgroup_t libqes_tests[] = { {"qes/util/", qes_util_tests}, {"qes/match/", qes_match_tests}, {"qes/file/", qes_file_tests}, {"qes/seqfile/", qes_seqfile_tests}, {"qes/seq/", qes_seq_tests}, {"qes/log/", qes_log_tests}, {"qes/sequtil/", qes_sequtil_tests}, {"testdata/", data_tests}, {"testhelpers/", helper_tests}, END_OF_GROUPS }; /* * === FUNCTION ============================================================= * Name: main * Description: Run all tests * ============================================================================ */ int main (int argc, const char *argv[]) { int res; int our_argc = argc; const char **our_argv = argv; data_prefix = NULL; if (argc>1) { data_prefix = strdup(argv[1]); our_argc -= 1; our_argv += 1; } if (data_prefix == NULL) { data_prefix = strdup("."); assert(data_prefix != NULL); } if (access(data_prefix, W_OK | X_OK | R_OK) != 0) { fprintf(stderr, "ERROR: Could not access data prefix dir '%s'\n", data_prefix); fprintf(stderr, "Usage: test_libqes []\n"); free(data_prefix); exit(EXIT_FAILURE); } res = tinytest_main(our_argc, our_argv, libqes_tests); free(data_prefix); return res; } libqes-0.1.21/test/test_file.c000066400000000000000000000351271263611052100161600ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_file.c * * Description: Test qes_file * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include static void test_qes_file_open (void *ptr) { struct qes_file *file = NULL; struct qes_file *badfile = NULL; char *fname = NULL; (void) ptr; /* Test file opening for reading */ fname = find_data_file("loremipsum.txt"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); tt_ptr_op(file, !=, NULL); tt_int_op(file->mode, ==, QES_FILE_MODE_READ); qes_file_close(file); free(fname); /* test zipped file opening for reading */ fname = find_data_file("loremipsum.txt.gz"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); tt_ptr_op(file, !=, NULL); tt_int_op(file->mode, ==, QES_FILE_MODE_READ); qes_file_close(file); free(fname); /* read with non-existant file */ fname = get_writable_file(); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); tt_ptr_op(file, ==, NULL); clean_writable_file(fname); fname = NULL; /* writing with gziped file */ fname = get_writable_file(); tt_assert(fname != NULL); file = qes_file_open(fname, "w"); tt_ptr_op(file, !=, NULL); tt_int_op(file->mode, ==, QES_FILE_MODE_WRITE); clean_writable_file(fname); fname = NULL; /* With non-existant file path */ badfile = qes_file_open("non/existent.file", "w"); tt_ptr_op(badfile, ==, NULL); end: qes_file_close(file); qes_file_close(badfile); if (fname != NULL) free(fname); } static void test_qes_file_close (void *ptr) { struct qes_file *file = NULL; struct qes_file *nullfile = NULL; char *fname = NULL; (void) ptr; /* Open file */ fname = find_data_file("loremipsum.txt"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); tt_assert(file); qes_file_close(file); tt_ptr_op(file, ==, NULL); /* check with null poitner, ensure no problems are caused. */ qes_file_close(nullfile); tt_ptr_op(nullfile, ==, NULL); end: qes_file_close(file); free(fname); } static void test_qes_file_rewind (void *ptr) { struct qes_file *file = NULL; size_t bufsize = 1<<10; char buffer[bufsize]; ssize_t res = 0; char *fname = NULL; (void) ptr; /* Open file */ fname = find_data_file("loremipsum.txt"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); tt_assert(file); while (res != EOF) { res = qes_file_readline(file, buffer, bufsize); } tt_int_op(file->filepos, ==, loremipsum_fsize); tt_int_op(QES_ZTELL(file->fp), ==, loremipsum_fsize); tt_assert(file->eof); tt_assert(file->feof); qes_file_rewind(file); tt_int_op(file->filepos, ==, 0); tt_assert(!file->eof); tt_assert(!file->feof); tt_int_op(QES_ZTELL(file->fp), ==, 0); end: qes_file_close(file); free(fname); } static void test_qes_file_readline (void *ptr) { struct qes_file *file = NULL; size_t bufsize = 1<<10; char buffer[bufsize]; ssize_t res_len = 0; off_t orig_filepos = 0; size_t iii; char *fname = NULL; (void) ptr; /* Open file */ fname = find_data_file("loremipsum.txt"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); /* Check each line is of the right length, that the length is returned, * that the string is as expected, and that file->filepos is updated. */ for (iii = 0; iii < n_loremipsum_lines; iii++) { orig_filepos = file->filepos; res_len = qes_file_readline(file, buffer, bufsize); tt_int_op(res_len, ==, strlen(buffer)); tt_int_op(res_len, ==, loremipsum_line_lens[iii]); tt_str_op(buffer, ==, loremipsum_lines[iii]); tt_int_op(file->filepos - orig_filepos, ==, loremipsum_line_lens[iii]); } /* Check that a file at EOF returns EOF. */ tt_int_op(file->filepos, ==, loremipsum_fsize); tt_int_op(qes_file_readline(file, buffer, bufsize), ==, EOF); tt_assert(file->eof) /* Test with bad parameters */ tt_int_op(qes_file_readline(NULL, buffer, bufsize), ==, -2); tt_int_op(qes_file_readline(file, NULL, bufsize), ==, -2); tt_int_op(qes_file_readline(file, buffer, 0), ==, -2); end: qes_file_close(file); free(fname); } static void test_qes_file_getuntil (void *ptr) { struct qes_file *file = NULL; const size_t bufsize = 1<<10; char buffer[bufsize]; ssize_t res_len = 0; size_t expt_len = 0; off_t orig_filepos = 0; off_t our_filepos = 0; size_t iii; const size_t n_delims = 5; const int delims[] = {' ', ',', '.', '\n', '\n'}; const char *delim_words[] = { "Lorem ", "ipsum dolor sit amet,", " consectetur adipiscing elit.", " Donec ornare tortor et\n", "rhoncus iaculis. Sed suscipit, arcu nec elementum vestibulum, tortor tortor\n", }; char *fname = NULL; (void) ptr; /* Open file */ fname = find_data_file("loremipsum.txt"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); /* Check each token is of the right length, that the length is returned, * that the string is as expected, and that file->filepos is updated. */ for (iii = 0; iii < n_delims; iii++) { orig_filepos = file->filepos; res_len = qes_file_getuntil(file, delims[iii], buffer, bufsize); our_filepos += res_len; expt_len = strnlen(delim_words[iii], bufsize); tt_int_op(res_len, ==, strnlen(buffer, bufsize)); tt_int_op(res_len, ==, expt_len); tt_str_op(buffer, ==, delim_words[iii]); tt_int_op(file->filepos - orig_filepos, ==, expt_len); tt_int_op(file->filepos, ==, our_filepos); } /* Check we can give EOF as the char and make it give us the remainder of the file */ orig_filepos = file->filepos; res_len = qes_file_getuntil(file, EOF, buffer, bufsize); expt_len = loremipsum_fsize - our_filepos; our_filepos += res_len; tt_int_op(res_len, ==, strnlen(buffer, bufsize)); tt_int_op(res_len, ==, expt_len); tt_int_op(file->filepos - orig_filepos, ==, expt_len); tt_int_op(file->filepos, ==, our_filepos); tt_assert(file->eof) tt_int_op(file->filepos, ==, loremipsum_fsize); /* Check that a file at EOF returns EOF. */ tt_int_op(file->filepos, ==, loremipsum_fsize); tt_int_op(qes_file_getuntil(file, '\n', buffer, bufsize), ==, EOF); tt_assert(file->eof) /* Test with bad parameters */ QES_ZREWIND(file->fp); file->eof = 0; file->filepos = 0; tt_int_op(qes_file_getuntil(NULL, '\n', buffer, bufsize), ==, -2); tt_int_op(qes_file_getuntil(file, 256, buffer, bufsize), ==, -2); tt_int_op(qes_file_getuntil(file, '\n', NULL, bufsize), ==, -2); tt_int_op(qes_file_getuntil(file, '\n', buffer, 0), ==, -2); end: qes_file_close(file); if (fname != NULL) free(fname); } static void test_qes_file_peek (void *ptr) { int res = 0; struct qes_file *file = NULL; off_t orig_filepos = 0; char *fname = NULL; (void) ptr; /* Open file and save pos */ fname = find_data_file("loremipsum.txt"); tt_assert(fname != NULL); file = qes_file_open(fname, "r"); orig_filepos = file->filepos; /* Peek a char */ res = qes_file_peek(file); /* Check it's the right char */ tt_int_op(res, ==, loremipsum_lines[0][0]); /* And that the filepos hasn't changed */ tt_int_op(file->filepos , ==, orig_filepos); /* And that the same char is returned again */ res = qes_file_peek(file); tt_int_op(res, ==, loremipsum_lines[0][0]); /* And that it returns an error on being given a null pointer */ tt_int_op(qes_file_peek(NULL), ==, -2); end: qes_file_close(file); if (fname != NULL) free(fname); } static void test_qes_file_guess_mode (void *ptr) { const char *modes[] = { "r", "rb", "rb8", "rT", "rbT", "w", "wb", "wb8", "wT", "wbT", "a", "ab", "ab8", "aT", "abT", "+", "+b", "+b8", "+T", "+bT", }; const int mode_results[] = { QES_FILE_MODE_READ, QES_FILE_MODE_READ, QES_FILE_MODE_READ, QES_FILE_MODE_READ, QES_FILE_MODE_READ, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN, }; const size_t num_modes = 20; size_t iii; (void) ptr; for (iii = 0; iii < num_modes; iii++) { tt_int_op(qes_file_guess_mode(modes[iii]), ==, mode_results[iii]); } end: ; } static void test_qes_file_readline_realloc (void *ptr) { char *buf = NULL; char *smallbuf = NULL; const size_t smallbuf_len = 4; const size_t buf_len = 1<<10; /* 1024b */ struct qes_file *file = NULL; ssize_t ret = 0; off_t fpos = 0; size_t line_num; char *nulcp = NULL; size_t tmpsz = buf_len; char *fname = NULL; (void) ptr; /* Open file and save pos */ fname = find_data_file("loremipsum.txt"); /* This should always work, so long as you run it from the right dir */ file = qes_file_open(fname, "r"); buf = calloc(buf_len, sizeof(*buf)); smallbuf = calloc(smallbuf_len, sizeof(*smallbuf)); tt_assert(file && buf && smallbuf); /* Check each line is of the right length, that the length is returned, * that the string is as expected, and that file->filepos is updated. */ for (line_num = 0; line_num < n_loremipsum_lines; line_num++) { ret = qes_file_readline_realloc(file, &buf, &tmpsz); fpos += ret; tt_int_op(fpos, ==, file->filepos); tt_str_op(buf, ==, loremipsum_lines[line_num]); tt_int_op(strlen(buf), ==, loremipsum_line_lens[line_num]); tt_int_op(ret, ==, loremipsum_line_lens[line_num]); tt_int_op(buf[ret], ==, '\0'); tt_int_op(tmpsz, ==, buf_len); tt_int_op(tmpsz, >=, qes_roundupz(loremipsum_line_lens[line_num])); } tt_int_op(file->filepos, ==, loremipsum_fsize); ret = qes_file_readline_realloc(file, &buf, &tmpsz); tt_assert(file->eof); tt_int_op(ret, ==, EOF); qes_file_close(file); /* * Test w/ small buffer */ /* Do the same checks, but with a buffer that needs resizing */ file = qes_file_open(fname, "r"); tmpsz = smallbuf_len; fpos = 0; for (line_num = 0; line_num < n_loremipsum_lines; line_num++) { ret = qes_file_readline_realloc(file, &smallbuf, &tmpsz); fpos += ret; tt_int_op(fpos, ==, file->filepos); tt_str_op(smallbuf, ==, loremipsum_lines[line_num]); tt_int_op(strlen(smallbuf), ==, loremipsum_line_lens[line_num]); tt_int_op(ret, ==, loremipsum_line_lens[line_num]); tt_int_op(tmpsz, !=, smallbuf_len); tt_int_op(tmpsz, >=, qes_roundupz(loremipsum_line_lens[line_num])); tt_int_op(smallbuf[ret], ==, '\0'); } tt_int_op(file->filepos, ==, loremipsum_fsize); /* Test with EOF file */ tmpsz = buf_len; ret = qes_file_readline_realloc(file, &buf, &tmpsz); tt_int_op(ret, ==, EOF); tt_str_op(buf, ==, ""); tt_int_op(strlen(buf), ==, 0); tt_int_op(tmpsz, ==, buf_len); tt_assert(file->eof) qes_file_close(file); /* * Test bad things */ /* Null buf. Should alloc a buffer and fill it */ file = qes_file_open(fname, "r"); line_num = 0; ret = qes_file_readline_realloc(file, &nulcp, &tmpsz); tt_int_op(ret, ==, loremipsum_line_lens[line_num]); tt_str_op(nulcp, ==, loremipsum_lines[line_num]); tt_int_op(strlen(nulcp), ==, loremipsum_line_lens[line_num]); tt_int_op(tmpsz, ==, __INIT_LINE_LEN); /* Null file */ ret = qes_file_readline_realloc(NULL, &buf, &tmpsz); tt_int_op(ret, ==, -2); /* This shouldn't change and is set in the prev. test */ tt_int_op(tmpsz, ==, __INIT_LINE_LEN); /* Both buf & file null */ ret = qes_file_readline_realloc(NULL, &nulcp, &tmpsz); tt_int_op(ret, ==, -2); tt_int_op(tmpsz, ==, __INIT_LINE_LEN); end: if (buf != NULL) free(buf); if (smallbuf != NULL) free(smallbuf); if (nulcp != NULL) free(nulcp); if (file != NULL) qes_file_close(file); free(fname); } static void test_qes_file_ok (void *ptr) { struct qes_file *file; char *writeable = NULL; char *readable = NULL; (void) ptr; readable = find_data_file("loremipsum.txt"); writeable = get_writable_file(); /* Should result in an OK file */ file = qes_file_open(readable, "r"); tt_assert(qes_file_ok(file)); tt_assert(qes_file_readable(file)); qes_file_close(file); file = qes_file_open("nosuchfile", "r"); tt_assert(!qes_file_ok(file)); tt_assert(!qes_file_readable(file)); qes_file_close(file); file = qes_file_open(writeable, "w"); tt_assert(qes_file_ok(file)); tt_assert(!qes_file_readable(file)); qes_file_close(file); end: if (file != NULL) qes_file_close(file); clean_writable_file(writeable); free(readable); } struct testcase_t qes_file_tests[] = { { "qes_file_open", test_qes_file_open, 0, NULL, NULL}, { "qes_file_peek", test_qes_file_peek, 0, NULL, NULL}, { "qes_file_readline", test_qes_file_readline, 0, NULL, NULL}, { "qes_file_readline_realloc", test_qes_file_readline_realloc, 0, NULL, NULL}, { "qes_file_guess_mode", test_qes_file_guess_mode, 0, NULL, NULL}, { "qes_file_close", test_qes_file_close, 0, NULL, NULL}, { "qes_file_rewind", test_qes_file_rewind, 0, NULL, NULL}, { "qes_file_getuntil", test_qes_file_getuntil, 0, NULL, NULL}, { "qes_file_ok", test_qes_file_ok, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_helpers.c000066400000000000000000000036161263611052100167010ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_helpers.c * * Description: Tests of test/helpers.c * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" static void test_crc32_file(void *data) { char *crc = NULL; char *fname = NULL; (void) data; fname = find_data_file("loremipsum.txt"); crc = crc32_file(fname); tt_str_op(crc, ==, "9f20f7ec"); end: free(fname); free(crc); } static void test_filecmp(void *data) { char *fname1 = NULL; char *fname2 = NULL; (void) data; fname1 = find_data_file("loremipsum.txt"); fname2 = find_data_file("loremipsum.txt.gz"); tt_int_op(filecmp(fname1, fname1), ==, 0); tt_int_op(filecmp(fname1, fname2), ==, 1); tt_int_op(filecmp(NULL, fname2), ==, -1); tt_int_op(filecmp("/does/not/exist/", fname2), ==, -1); end: free(fname1); free(fname2); } struct testcase_t helper_tests[] = { { "crc32_file", test_crc32_file, 0, NULL, NULL}, { "filecmp", test_filecmp, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_log.c000066400000000000000000000136071263611052100160210ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_log.c * * Description: Test logging * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include #include static void test_qes_logger_setup(void *ptr) { int res = 0; struct qes_logger *logger = NULL; (void) ptr; /* Test that when created, the logger has logical initial values */ logger = qes_logger_create(); tt_ptr_op(logger, !=, NULL); tt_ptr_op(logger->destinations, ==, NULL); tt_ptr_op(logger->name, ==, NULL); tt_int_op(logger->n_destinations, ==, 0); tt_int_op(logger->level, ==, QES_LOG_DEBUG); tt_int_op(logger->lock, ==, 0); /* Add a destination, check it is there */ res = qes_logger_add_destination(logger, stderr, QES_LOG_ERROR); tt_int_op(res, ==, 0); tt_ptr_op(logger->destinations, !=, NULL); tt_ptr_op(logger->destinations[0].stream, ==, stderr); tt_int_op(logger->destinations[0].level, ==, QES_LOG_ERROR); tt_int_op(logger->n_destinations, ==, 1); qes_logger_destroy(logger); tt_ptr_op(logger, ==, NULL); end: if (logger != NULL) { if (logger->destinations != NULL) free(logger->destinations); if (logger->name != NULL) free(logger->name); free(logger); } } static void test_qes_logger_init(void *ptr) { int res = 0; struct qes_logger *logger = NULL; (void) ptr; logger = qes_logger_create(); tt_ptr_op(logger, !=, NULL); /* Test the init function sets values correctly */ res = qes_logger_init(logger, "test logger", QES_LOG_INFO); tt_int_op(res, ==, 0); tt_ptr_op(logger->name, !=, NULL); tt_int_op(logger->level, ==, QES_LOG_INFO); tt_int_op(logger->lock, ==, 0); /* test that we error out if we give init NULL */ res = qes_logger_init(NULL, "test logger", QES_LOG_INFO); tt_int_op(res, ==, 1); /* Test that we silently set logger->name to NULL if we pass NULL */ res = qes_logger_init(logger, NULL, QES_LOG_INFO); tt_int_op(res, ==, 0); tt_ptr_op(logger->name, ==, NULL); end: if (logger != NULL) { if (logger->destinations != NULL) free(logger->destinations); if (logger->name != NULL) free(logger->name); free(logger); } } static void test_qes_logger_logging(void *ptr) { int res = 0; struct qes_logger *logger = NULL; char *log_fname = NULL; char *truth_fname = NULL; FILE *log_file = NULL; (void) ptr; /* Set up a logger, with an actual file as output */ logger = qes_logger_create(); tt_ptr_op(logger, !=, NULL); truth_fname = find_data_file("truth/log_test.txt"); tt_ptr_op(truth_fname, !=, NULL); log_fname = get_writable_file(); tt_ptr_op(log_fname, !=, NULL); log_file = fopen(log_fname, "w"); tt_ptr_op(log_file, !=, NULL); res = qes_logger_add_destination(logger, log_file, QES_LOG_INFO); tt_int_op(res, ==, 0); /* Test printing to the file using the message functions */ qes_log_message_debug(logger, "Hello World\n"); /* wont' print */ qes_log_message_info(logger, "Hello World\n"); /* should print */ /* Test printing to the file with the format functions */ qes_log_format_debug(logger, "%s\n", "Hello World"); qes_log_format_info(logger, "%s\n", "Hello World"); /* Test the output file was created correctly */ tt_int_op(filecmp(log_fname, truth_fname), ==, 0); end: if (log_file != NULL) fclose(log_file); if (truth_fname != NULL) free(truth_fname); if (log_fname != NULL) free(log_fname); qes_logger_destroy(logger); } static void test_qes_log_entry(void *ptr) { int res = 0; struct qes_log_entry *entry = NULL; (void) ptr; /* Test that create gives us a valid entry with sane defaults */ entry = qes_log_entry_create(); tt_ptr_op(entry, !=, NULL); tt_ptr_op(entry->message, ==, NULL); tt_int_op(entry->level, ==, QES_LOG_DEBUG); /* Check that init fills the entry appropriately */ res = qes_log_entry_init(entry, QES_LOG_ERROR, "Test"); tt_int_op(res, ==, 0); tt_ptr_op(entry, !=, NULL); tt_str_op(entry->message, ==, "Test"); tt_int_op(entry->level, ==, QES_LOG_ERROR); /* test that clear clears an entry, without freeing the entry itself */ qes_log_entry_clear(entry); tt_ptr_op(entry, !=, NULL); tt_ptr_op(entry->message, ==, NULL); tt_int_op(entry->level, ==, QES_LOG_DEBUG); /* test formatting an entry */ res = qes_log_entry_format(entry, QES_LOG_ERROR, "%s", "Test"); tt_int_op(res, ==, 0); tt_ptr_op(entry, !=, NULL); tt_str_op(entry->message, ==, "Test"); tt_int_op(entry->level, ==, QES_LOG_ERROR); qes_log_entry_destroy(entry); tt_ptr_op(entry, ==, NULL); end: qes_log_entry_destroy(entry); } struct testcase_t qes_log_tests[] = { { "qes_logger_setup", test_qes_logger_setup, 0, NULL, NULL}, { "qes_logger_init", test_qes_logger_init, 0, NULL, NULL}, { "qes_logger_logging", test_qes_logger_logging, 0, NULL, NULL}, { "qes_log_entry", test_qes_log_entry, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_match.c000066400000000000000000000105171263611052100163310ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_match.c * * Description: Test qes_match functions * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include #include static void test_qes_hamming (void *p) { (void) (p); /* Simple stuff */ tt_int_op(qes_match_hamming("ACTTG", "ACTTG", 5), ==, 0); tt_int_op(qes_match_hamming("ACTTG", "ACTGG", 5), ==, 1); /* Different lengths */ tt_int_op(qes_match_hamming("ACTTGA", "ACTTG", 5), ==, 0); tt_int_op(qes_match_hamming("ACTTG", "ACTTGA", 5), ==, 0); tt_int_op(qes_match_hamming("ACTTG", "ACTGGA", 5), ==, 1); tt_int_op(qes_match_hamming("ACTTG", "ACTGGA", 6), ==, 2); tt_int_op(qes_match_hamming("ACTTG", "ACTTGA", 6), ==, 1); /* Make it guess lengths */ tt_int_op(qes_match_hamming("ACTTG", "ACTTG", 0), ==, 0); tt_int_op(qes_match_hamming("ACATG", "ACTTG", 0), ==, 1); tt_int_op(qes_match_hamming("ACTTG", "ACTTGT", 0), ==, 0); tt_int_op(qes_match_hamming("ACATG", "ACTTGT", 0), ==, 1); tt_int_op(qes_match_hamming("ACTTGT", "ACTTG", 0), ==, 0); /* Give it hell */ tt_int_op(qes_match_hamming("ACTTG", NULL, 0), ==, -1); tt_int_op(qes_match_hamming(NULL, "ACTTG", 0), ==, -1); tt_int_op(qes_match_hamming(NULL, NULL, 0), ==, -1); end: ; } static void test_qes_hamming_max (void *p) { (void) (p); /* Same tests as per hamming, max is INT_MAX */ /* Simple stuff */ tt_int_op(qes_match_hamming_max("ACTTG", "ACTTG", 5, INT_MAX), ==, 0); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGG", 5, INT_MAX), ==, 1); /* Different lengths */ tt_int_op(qes_match_hamming_max("ACTTGA", "ACTTG", 5, INT_MAX), ==, 0); tt_int_op(qes_match_hamming_max("ACTTG", "ACTTGA", 5, INT_MAX), ==, 0); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGGA", 5, INT_MAX), ==, 1); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGGA", 6, INT_MAX), ==, 2); tt_int_op(qes_match_hamming_max("ACTTG", "ACTTGA", 6, INT_MAX), ==, 1); /* Make it guess lengths */ tt_int_op(qes_match_hamming_max("ACTTG", "ACTTG", 0, INT_MAX), ==, 0); tt_int_op(qes_match_hamming_max("ACATG", "ACTTG", 0, INT_MAX), ==, 1); tt_int_op(qes_match_hamming_max("ACTTG", "ACTTGT", 0, INT_MAX), ==, 0); tt_int_op(qes_match_hamming_max("ACATG", "ACTTGT", 0, INT_MAX), ==, 1); tt_int_op(qes_match_hamming_max("ACTTGT", "ACTTG", 0, INT_MAX), ==, 0); /* Test it bails out when over ``max`` */ tt_int_op(qes_match_hamming_max("ACTTG", "ACTGG", 5, 1), ==, 1); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGG", 5, 0), ==, 1); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGA", 5, 0), ==, 1); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGA", 5, 1), ==, 2); tt_int_op(qes_match_hamming_max("ACTTG", "ACTGA", 5, 2), ==, 2); /* Give it hell */ tt_int_op(qes_match_hamming_max("ACTTG", NULL, 0, INT_MAX), ==, -1); tt_int_op(qes_match_hamming_max(NULL, "ACTTG", 0, INT_MAX), ==, -1); tt_int_op(qes_match_hamming_max(NULL, NULL, 0, INT_MAX), ==, -1); tt_int_op(qes_match_hamming_max("ACTTG", "ACTTG", 0, -1), ==, -1); tt_int_op(qes_match_hamming_max("ACTTG", NULL, 0, -1), ==, -1); tt_int_op(qes_match_hamming_max(NULL, "ACTTG", 0, -1), ==, -1); tt_int_op(qes_match_hamming_max(NULL, NULL, 0, -1), ==, -1); end: ; } struct testcase_t qes_match_tests[] = { { "qes_match_hamming", test_qes_hamming, 0, NULL, NULL}, { "qes_match_hamming_max", test_qes_hamming_max, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_seq.c000066400000000000000000000406431263611052100160300ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_seq.c * * Description: Test qes_seq.c * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include static void test_qes_seq_create (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; tt_ptr_op(seq, ==, NULL); seq = qes_seq_create(); tt_ptr_op(seq, !=, NULL); tt_ptr_op(seq->name.str, !=, NULL); tt_int_op(seq->name.capacity, >, 0); tt_int_op(seq->name.len, ==, 0); tt_ptr_op(seq->comment.str, !=, NULL); tt_int_op(seq->comment.capacity, >, 0); tt_int_op(seq->comment.len, ==, 0); tt_ptr_op(seq->seq.str, !=, NULL); tt_int_op(seq->seq.capacity, >, 0); tt_int_op(seq->seq.len, ==, 0); tt_ptr_op(seq->qual.str, !=, NULL); tt_int_op(seq->qual.capacity, >, 0); tt_int_op(seq->qual.len, ==, 0); tt_assert(qes_str_ok(&seq->name)); tt_assert(qes_str_ok(&seq->comment)); tt_assert(qes_str_ok(&seq->seq)); tt_assert(qes_str_ok(&seq->qual)); end: qes_seq_destroy(seq); } static void test_qes_seq_create_no_qual (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; tt_ptr_op(seq, ==, NULL); seq = qes_seq_create_no_qual(); tt_ptr_op(seq, !=, NULL); tt_ptr_op(seq->name.str, !=, NULL); tt_int_op(seq->name.capacity, >, 0); tt_int_op(seq->name.len, ==, 0); tt_ptr_op(seq->comment.str, !=, NULL); tt_int_op(seq->comment.capacity, >, 0); tt_int_op(seq->comment.len, ==, 0); tt_ptr_op(seq->seq.str, !=, NULL); tt_int_op(seq->seq.capacity, >, 0); tt_int_op(seq->seq.len, ==, 0); tt_ptr_op(seq->qual.str, ==, NULL); tt_int_op(seq->qual.capacity, ==, 0); tt_int_op(seq->qual.len, ==, 0); tt_assert(qes_str_ok(&seq->name)); tt_assert(qes_str_ok(&seq->comment)); tt_assert(qes_str_ok(&seq->seq)); tt_assert(!qes_str_ok(&seq->qual)); end: qes_seq_destroy(seq); } static void test_qes_seq_create_no_qual_or_comment (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; tt_ptr_op(seq, ==, NULL); seq = qes_seq_create_no_qual_or_comment(); tt_ptr_op(seq, !=, NULL); tt_ptr_op(seq->name.str, !=, NULL); tt_int_op(seq->name.capacity, >, 0); tt_int_op(seq->name.len, ==, 0); tt_ptr_op(seq->comment.str, ==, NULL); tt_int_op(seq->comment.capacity, ==, 0); tt_int_op(seq->comment.len, ==, 0); tt_ptr_op(seq->seq.str, !=, NULL); tt_int_op(seq->seq.capacity, >, 0); tt_int_op(seq->seq.len, ==, 0); tt_ptr_op(seq->qual.str, ==, NULL); tt_int_op(seq->qual.capacity, ==, 0); tt_int_op(seq->qual.len, ==, 0); tt_assert(qes_str_ok(&seq->name)); tt_assert(!qes_str_ok(&seq->comment)); tt_assert(qes_str_ok(&seq->seq)); tt_assert(!qes_str_ok(&seq->qual)); end: qes_seq_destroy(seq); } static void test_qes_seq_ok (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; /* Test null seq */ tt_assert(!qes_seq_ok(seq)); /* Make valid seq */ seq = qes_seq_create(); tt_assert(qes_seq_ok(seq)); /* invalidate name, should fail */ qes_str_destroy_cp(&seq->name); tt_assert(!qes_seq_ok(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok(seq)); /* invalidate comment, should fail */ qes_str_destroy_cp(&seq->comment); tt_assert(!qes_seq_ok(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok(seq)); /* invalidate seq, should fail */ qes_str_destroy_cp(&seq->seq); tt_assert(!qes_seq_ok(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok(seq)); /* invalidate qual, should fail */ qes_str_destroy_cp(&seq->qual); tt_assert(!qes_seq_ok(seq)); qes_seq_destroy(seq); /* Destroy seq, invalidating it */ qes_seq_destroy(seq); tt_assert(!qes_seq_ok(seq)); end: qes_seq_destroy(seq); } static void test_qes_seq_ok_no_comment (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; /* Test null seq */ tt_assert(!qes_seq_ok_no_comment(seq)); /* Make valid seq */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment(seq)); /* invalidate name, should fail */ qes_str_destroy_cp(&seq->name); tt_assert(!qes_seq_ok_no_comment(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment(seq)); /* invalidate comment, should still pass */ qes_str_destroy_cp(&seq->comment); tt_assert(qes_seq_ok_no_comment(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment(seq)); /* invalidate seq, should fail */ qes_str_destroy_cp(&seq->seq); tt_assert(!qes_seq_ok_no_comment(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment(seq)); /* invalidate qual, should fail */ qes_str_destroy_cp(&seq->qual); tt_assert(!qes_seq_ok_no_comment(seq)); qes_seq_destroy(seq); /* Destroy seq, invalidating it */ qes_seq_destroy(seq); tt_assert(!qes_seq_ok_no_comment(seq)); end: qes_seq_destroy(seq); } static void test_qes_seq_ok_no_qual (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; /* Test null seq */ tt_assert(!qes_seq_ok_no_qual(seq)); /* Make valid seq */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_qual(seq)); /* invalidate name, should fail */ qes_str_destroy_cp(&seq->name); tt_assert(!qes_seq_ok_no_qual(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_qual(seq)); /* invalidate comment, should fail */ qes_str_destroy_cp(&seq->comment); tt_assert(!qes_seq_ok_no_qual(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_qual(seq)); /* invalidate seq, should fail */ qes_str_destroy_cp(&seq->seq); tt_assert(!qes_seq_ok_no_qual(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_qual(seq)); /* invalidate qual, should PASS */ qes_str_destroy_cp(&seq->qual); tt_assert(qes_seq_ok_no_qual(seq)); qes_seq_destroy(seq); /* Destroy seq, invalidating it */ qes_seq_destroy(seq); tt_assert(!qes_seq_ok_no_qual(seq)); end: qes_seq_destroy(seq); } static void test_qes_seq_print(void *ptr) { struct qes_seq *seq = NULL; FILE *fp = NULL; char *outfile = NULL; char *truthfile = NULL; int res = 1; (void) ptr; /* Create output file */ outfile = get_writable_file(); fp = fopen(outfile, "w"); tt_ptr_op(fp, !=, NULL); /* create sequence, fill it */ seq = qes_seq_create(); res = qes_seq_fill(seq, "TEST", "Comment 1", "AGCT", "IIII"); tt_int_op(res, ==, 0); /* Print the seq to the output file */ res = qes_seq_print(seq, fp); tt_int_op(res, ==, 0); /* Check printing */ truthfile = find_data_file("truth/qes_seq_print.fq"); tt_ptr_op(truthfile, !=, NULL); tt_int_op(filecmp(outfile, truthfile), ==, 0); /* Clean up */ free(truthfile); truthfile = NULL; fclose(fp); fp = NULL; qes_seq_destroy(seq); /* recreate, just without quality */ seq = qes_seq_create(); fp = fopen(outfile, "w"); tt_ptr_op(fp, !=, NULL); res = qes_seq_fill(seq, "TEST", "Comment 1", "AGCT", ""); tt_int_op(res, ==, 0); /* Print the seq to the output file */ res = qes_seq_print(seq, fp); tt_int_op(res, ==, 0); /* Check printing */ truthfile = find_data_file("truth/qes_seq_print.fa"); tt_ptr_op(truthfile, !=, NULL); tt_int_op(filecmp(outfile, truthfile), ==, 0); free(truthfile); truthfile = NULL; fclose(fp); fp = NULL; /* error cases */ tt_int_op(qes_seq_print(NULL, stdout), ==, 1); tt_int_op(qes_seq_print(seq, NULL), ==, 1); end: qes_seq_destroy(seq); if (fp != NULL) fclose(fp); if (outfile != NULL) free(outfile); if (truthfile != NULL) free(truthfile); } static void test_qes_seq_ok_no_comment_or_qual (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; /* Test null seq */ tt_assert(!qes_seq_ok_no_comment_or_qual(seq)); /* Make valid seq */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment_or_qual(seq)); /* invalidate name, should fail */ qes_str_destroy_cp(&seq->name); tt_assert(!qes_seq_ok_no_comment_or_qual(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment_or_qual(seq)); /* invalidate comment, should still pass */ qes_str_destroy_cp(&seq->comment); tt_assert(qes_seq_ok_no_comment_or_qual(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment_or_qual(seq)); /* invalidate seq, should fail */ qes_str_destroy_cp(&seq->seq); tt_assert(!qes_seq_ok_no_comment_or_qual(seq)); qes_seq_destroy(seq); /* remake */ seq = qes_seq_create(); tt_assert(qes_seq_ok_no_comment_or_qual(seq)); /* invalidate qual, should fail */ qes_str_destroy_cp(&seq->qual); tt_assert(qes_seq_ok_no_comment_or_qual(seq)); qes_seq_destroy(seq); /* Destroy seq, invalidating it */ qes_seq_destroy(seq); tt_assert(!qes_seq_ok_no_comment_or_qual(seq)); end: qes_seq_destroy(seq); } static void test_qes_seq_destroy (void *ptr) { struct qes_seq *seq = NULL; (void) ptr; tt_ptr_op(seq, ==, NULL); seq = qes_seq_create(); tt_ptr_op(seq, !=, NULL); qes_seq_destroy(seq); tt_ptr_op(seq, ==, NULL); seq = NULL; /* Best be sure */ qes_seq_destroy(seq); end: qes_seq_destroy(seq); } static void test_qes_seq_copy(void *ptr) { struct qes_seq *seq = NULL; struct qes_seq *copy = NULL; int res = 1; (void) ptr; seq = qes_seq_create(); copy = qes_seq_create(); res = qes_seq_fill(seq, "TEST", "Comment 1", "AGCT", "IIII"); tt_int_op(res, ==, 0); tt_str_op(seq->name.str, ==, "TEST"); tt_str_op(seq->comment.str, ==, "Comment 1"); tt_str_op(seq->seq.str, ==, "AGCT"); tt_str_op(seq->qual.str, ==, "IIII"); res = qes_seq_copy(copy, seq); tt_int_op(res, ==, 0); tt_str_op(copy->name.str, ==, "TEST"); tt_str_op(copy->comment.str, ==, "Comment 1"); tt_str_op(copy->seq.str, ==, "AGCT"); tt_str_op(copy->qual.str, ==, "IIII"); tt_int_op(qes_seq_copy(NULL, seq), ==, 1); tt_int_op(qes_seq_copy(seq, NULL), ==, 1); tt_int_op(qes_seq_copy(seq, seq), ==, 1); end: qes_seq_destroy(seq); qes_seq_destroy(copy); } static void test_qes_seq_fill_funcs(void *ptr) { #define CHECK_FILLING(submember, st, ln) \ seq = qes_seq_create(); \ tt_str_op(seq->submember.str, ==, ""); \ res = qes_seq_fill_ ##submember (seq, st, ln); \ tt_int_op(res, ==, 0); \ tt_str_op(seq->submember.str, ==, st); \ tt_int_op(seq->submember.len, ==, ln); \ tt_int_op(seq->submember.capacity, >=, ln); \ qes_seq_destroy(seq); #define CHECK_FILLING_FAIL(submember, st, ln) \ seq = qes_seq_create(); \ tt_str_op(seq->submember.str, ==, ""); \ res = qes_seq_fill_ ##submember (seq, st, ln); \ tt_int_op(res, ==, 1); \ tt_str_op(seq->submember.str, ==, ""); \ tt_int_op(seq->submember.len, ==, 0); \ qes_seq_destroy(seq); struct qes_seq *seq = NULL; int res = 0; char *tmp = NULL; (void) ptr; /* These should all work pretty well */ CHECK_FILLING(name, "HWI_TEST", 8) CHECK_FILLING(comment, "abc 123 comment", 15) CHECK_FILLING(seq, "ACTG", 4) CHECK_FILLING(qual, "IIII", 4) /* These should all fail */ CHECK_FILLING_FAIL(name, NULL, 1) CHECK_FILLING_FAIL(name, "BAD", 0) CHECK_FILLING_FAIL(comment, NULL, 1) CHECK_FILLING_FAIL(comment, "BAD", 0) CHECK_FILLING_FAIL(seq, NULL, 1) CHECK_FILLING_FAIL(seq, "BAD", 0) CHECK_FILLING_FAIL(qual, NULL, 1) CHECK_FILLING_FAIL(qual, "BAD", 0) tt_int_op(qes_seq_fill_name(NULL, "BAD", 3), ==, 1); tt_int_op(qes_seq_fill_comment(NULL, "BAD", 3), ==, 1); tt_int_op(qes_seq_fill_seq(NULL, "BAD", 3), ==, 1); tt_int_op(qes_seq_fill_qual(NULL, "BAD", 3), ==, 1); /* Fill header */ #define CHECK_FILL_HEADER(st, ln, nm, nmlen, com, comlen) \ tmp = strdup(st); \ seq = qes_seq_create(); \ tt_str_op(seq->name.str, ==, ""); \ tt_str_op(seq->comment.str, ==, ""); \ res = qes_seq_fill_header(seq, tmp, ln); \ tt_int_op(res, ==, 0); \ tt_str_op(seq->name.str, ==, nm); \ tt_int_op(seq->name.len, ==, nmlen); \ tt_int_op(seq->name.capacity, >=, nmlen); \ tt_str_op(seq->comment.str, ==, com); \ tt_int_op(seq->comment.len, ==, comlen); \ tt_int_op(seq->comment.capacity, >=, comlen); \ qes_seq_destroy(seq); \ free(tmp); \ tmp = NULL; CHECK_FILL_HEADER("@HWI_TEST COMM\n", 15, "HWI_TEST", 8, "COMM", 4) CHECK_FILL_HEADER("@HWI_TEST COMM\n", 0, "HWI_TEST", 8, "COMM", 4) CHECK_FILL_HEADER("@HWI_TEST COMM \r\n", 17, "HWI_TEST", 8, "COMM", 4) CHECK_FILL_HEADER("@HWI_TEST COMM", 14, "HWI_TEST", 8, "COMM", 4) CHECK_FILL_HEADER(">HWI_TEST COMM", 14, "HWI_TEST", 8, "COMM", 4) CHECK_FILL_HEADER("HWI_TEST COMM", 13, "HWI_TEST", 8, "COMM", 4) CHECK_FILL_HEADER("@HWI_TEST", 9, "HWI_TEST", 8, "", 0) CHECK_FILL_HEADER(">HWI_TEST", 9, "HWI_TEST", 8, "", 0) CHECK_FILL_HEADER("HWI_TEST", 8, "HWI_TEST", 8, "", 0) /* Check bad values */ seq = qes_seq_create(); tmp = strdup("BAD"); tt_int_op(qes_seq_fill_header(NULL, tmp, 3), ==, 1); tt_int_op(qes_seq_fill_header(seq, NULL, 3), ==, 1); qes_seq_destroy(seq); end: if (tmp != NULL) { free(tmp); } qes_seq_destroy(seq); #undef CHECK_FILLING #undef CHECK_FILLING_FAIL #undef CHECK_FILL_HEADER } struct testcase_t qes_seq_tests[] = { { "qes_seq_create", test_qes_seq_create, 0, NULL, NULL}, { "qes_seq_create_no_qual", test_qes_seq_create_no_qual, 0, NULL, NULL}, { "qes_seq_create_no_qual_or_comment", test_qes_seq_create_no_qual_or_comment, 0, NULL, NULL}, { "qes_seq_ok", test_qes_seq_ok, 0, NULL, NULL}, { "qes_seq_ok_no_comment", test_qes_seq_ok_no_comment, 0, NULL, NULL}, { "qes_seq_ok_no_qual", test_qes_seq_ok_no_qual, 0, NULL, NULL}, { "qes_seq_ok_no_comment_or_qual", test_qes_seq_ok_no_comment_or_qual, 0, NULL, NULL}, { "qes_seq_destroy", test_qes_seq_destroy, 0, NULL, NULL}, { "qes_seq_fill", test_qes_seq_fill_funcs, 0, NULL, NULL}, { "qes_seq_copy", test_qes_seq_copy, 0, NULL, NULL}, { "qes_seq_print", test_qes_seq_print, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_seqfile.c000066400000000000000000000344771263611052100167000ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_seqfile.c * * Description: Tests for the qes_seqfile module * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include #include "kseq.h" #ifdef ZLIB_FOUND # include KSEQ_INIT(gzFile, gzread) #else # include # include KSEQ_INIT(int, read) #endif static void test_qes_seqfile_create(void *ptr) { struct qes_seqfile *sf = NULL; char *fname = NULL; (void) ptr; /* Test file opening for reading */ /* test opening a valid, unziped FASTQ */ fname = find_data_file("test.fastq"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); tt_ptr_op(sf, !=, NULL); tt_ptr_op(sf->qf, !=, NULL); tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_READ); tt_int_op(sf->n_records, ==, 0); tt_int_op(sf->format, ==, FASTQ_FMT); qes_seqfile_destroy(sf); free(fname); /* test opening a valid, unziped FASTA */ fname = find_data_file("test.fasta"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); tt_ptr_op(sf, !=, NULL); tt_ptr_op(sf->qf, !=, NULL); tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_READ); tt_int_op(sf->n_records, ==, 0); tt_int_op(sf->format, ==, FASTA_FMT); qes_seqfile_destroy(sf); free(fname); /* Test opening a file in transparent write mode */ fname = get_writable_file(); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "wT"); QES_ZWRITE(sf->qf->fp, "ABCD", 4); tt_ptr_op(sf, !=, NULL); tt_ptr_op(sf->qf, !=, NULL); tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_WRITE); tt_int_op(sf->n_records, ==, 0); tt_int_op(access(fname, F_OK), ==, 0); qes_seqfile_destroy(sf); clean_writable_file(fname); fname = NULL; /* Test opening a file in write mode , acually zipping output */ fname = get_writable_file(); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "w9"); tt_ptr_op(sf, !=, NULL); tt_ptr_op(sf->qf, !=, NULL); tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_WRITE); tt_int_op(sf->n_records, ==, 0); tt_int_op(access(fname, F_OK), ==, 0); qes_seqfile_destroy(sf); clean_writable_file(fname); fname = NULL; end: qes_seqfile_destroy(sf); if (fname != NULL) { free(fname); } } static void test_qes_seqfile_guess_format (void *ptr) { struct qes_seqfile *sf = NULL; int res = -1; char *fname = NULL; (void) ptr; /* Test file opening for reading */ fname = find_data_file("test.fastq"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); /* test with a FASTQ file */ res = qes_seqfile_guess_format(sf); tt_int_op(res, ==, FASTQ_FMT); tt_int_op(sf->format, ==, FASTQ_FMT); qes_seqfile_destroy(sf); free(fname); /* test with a FASTA file */ fname = find_data_file("test.fasta"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); res = qes_seqfile_guess_format(sf); tt_int_op(res, ==, FASTA_FMT); tt_int_op(sf->format, ==, FASTA_FMT); qes_seqfile_destroy(sf); free(fname); fname = NULL; #ifdef ZLIB_FOUND /* test with a gziped FASTQ file */ fname = find_data_file("test.fastq.gz"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); res = qes_seqfile_guess_format(sf); tt_int_op(res, ==, FASTQ_FMT); tt_int_op(sf->format, ==, FASTQ_FMT); qes_seqfile_destroy(sf); #endif end: qes_seqfile_destroy(sf); if (fname != NULL) free(fname); } static void test_qes_seqfile_destroy (void *ptr) { struct qes_seqfile *sf = NULL; char *fname = NULL; (void) ptr; /* Test file opening for reading */ fname = find_data_file("test.fastq"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); tt_ptr_op(sf, !=, NULL); tt_assert(qes_seqfile_ok(sf)); qes_seqfile_destroy(sf); tt_ptr_op(sf, ==, NULL); tt_assert(!qes_seqfile_ok(sf)); end: qes_seqfile_destroy(sf); if (fname != NULL) free(fname); } /*=== FUNCTION ============================================================* Name: test_qes_seqfile_read Description: Tests the qes_seqfile_read function from qes_seqfile.c *===========================================================================*/ static void test_qes_seqfile_read (void *ptr) { struct qes_seq *seq = qes_seq_create(); ssize_t res = 0; struct qes_seqfile *sf = NULL; char *fname = NULL; /* Check a seq is empty */ #define CHECK_SEQ_EMPTY \ tt_str_op(seq->name.str, ==, ""); \ tt_str_op(seq->comment.str, ==, ""); \ tt_str_op(seq->seq.str, ==, ""); \ tt_str_op(seq->qual.str, ==, "") /* Check seq against the first known read */ #define CHECK_SEQ_FIRST \ tt_str_op(seq->name.str, ==, first_fastq_read[0]); \ tt_str_op(seq->comment.str, ==, first_fastq_read[1]); \ tt_str_op(seq->seq.str, ==, first_fastq_read[2]); \ tt_str_op(seq->qual.str, ==, first_fastq_read[3]) /* Open, read, check & close a seqfile */ #define CHECK_SEQFILE_READ(fn, expt_res, check_seq) \ fname = find_data_file(fn); \ tt_assert(fname != NULL); \ sf = qes_seqfile_create(fname, "r"); \ res = qes_seqfile_read(sf, seq); \ tt_int_op(res, ==, expt_res); \ check_seq; \ qes_seqfile_destroy(sf); \ free(fname); \ fname = NULL /* Open, read, check & close a seqfile, forcing its filetype to FASTQ */ #define CHECK_SEQFILE_READ_FORCE(fn, expt_res, check_seq) \ fname = find_data_file(fn); \ tt_assert(fname != NULL); \ sf = qes_seqfile_create(fname, "r"); \ qes_seqfile_set_format(sf, FASTQ_FMT); \ res = qes_seqfile_read(sf, seq); \ tt_int_op(res, ==, expt_res); \ check_seq; \ qes_seqfile_destroy(sf); \ free(fname); \ fname = NULL (void) ptr; /* Test file opening for reading */ CHECK_SEQFILE_READ("test.fastq", first_fastq_len, CHECK_SEQ_FIRST); CHECK_SEQFILE_READ("test.fasta", 33, tt_str_op(seq->name.str, ==, "HWI-ST960:105:D10GVACXX:2:1101:1122:2186"); tt_str_op(seq->comment.str, ==, "1:N:0: bcd:RPI8 seq:CACACTTGAATC"); tt_str_op(seq->seq.str, ==, "CACACTTGAATCCAGTTTAAAGTTAACTCATTG"); tt_int_op(seq->qual.len, ==, 0); tt_str_op(seq->qual.str, ==, "") ); CHECK_SEQFILE_READ("nocomment.fasta", 33, tt_str_op(seq->name.str, ==, "HWI-ST960:105:D10GVACXX:2:1101:1122:2186"); tt_int_op(seq->comment.len, ==, 0); tt_str_op(seq->comment.str, ==, ""); tt_str_op(seq->seq.str, ==, "CACACTTGAATCCAGTTTAAAGTTAACTCATTG"); tt_int_op(seq->qual.len, ==, 0); tt_str_op(seq->qual.str, ==, "") ); /* Test with bad fastqs, ensure all code paths are taken */ CHECK_SEQFILE_READ("loremipsum.txt", -2, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("bad_nohdr.fastq", -2, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("loremipsum.txt", -2, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ_FORCE("loremipsum.txt", -3, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("empty.fastq", -3, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("bad_noqual.fastq", -6, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("bad_noqualhdrchr.fastq", -5, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("bad_noqualhdreol.fastq", -5, CHECK_SEQ_EMPTY); CHECK_SEQFILE_READ("bad_diff_lens.fastq", -7, CHECK_SEQ_EMPTY); /* Check with bad params that it returns -2 */ res = qes_seqfile_read(NULL, seq); tt_int_op(res, ==, -2); res = qes_seqfile_read(sf, NULL); tt_int_op(res, ==, -2); end: qes_seqfile_destroy(sf); qes_seq_destroy(seq); if (fname != NULL) { free(fname); } #undef CHECK_SEQ_EMPTY #undef CHECK_SEQFILE_READ } static void test_qes_seqfile_read_vs_kseq (void *ptr) { struct qes_seq *seq = qes_seq_create(); #ifdef ZLIB_FOUND char *fname = find_data_file("test.fastq.gz"); gzFile fp = gzopen(fname, "r"); #else char *fname = find_data_file("test.fastq"); int fp = open(fname, O_RDONLY); #endif struct qes_seqfile *sf = qes_seqfile_create(fname, "r"); kseq_t *kseq = kseq_init(fp); ssize_t kseq_res = 0; ssize_t my_res = 0; (void) ptr; tt_assert(fname != NULL); while (1) { my_res = qes_seqfile_read(sf, seq); kseq_res = kseq_read(kseq); tt_int_op(my_res, ==, kseq_res); if (my_res < 1 || kseq_res < 1) { /* EOF or error */ break; } tt_str_op(seq->name.str, ==, kseq->name.s); tt_str_op(seq->comment.str, ==, kseq->comment.s); tt_str_op(seq->seq.str, ==, kseq->seq.s); tt_str_op(seq->qual.str, ==, kseq->qual.s); } my_res = qes_seqfile_read(sf, seq); kseq_res = kseq_read(kseq); tt_int_op(my_res, ==, kseq_res); tt_int_op(my_res, ==, EOF); qes_seqfile_destroy(sf); qes_seq_destroy(seq); kseq_destroy(kseq); kseq = NULL; #ifdef ZLIB_FOUND gzclose(fp); #else close(fp); #endif free(fname); /* Try again, with fasta */ seq = qes_seq_create(); fname = find_data_file("test.fasta"); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "r"); #ifdef ZLIB_FOUND fp = gzopen(fname, "r"); #else fp = open(fname, O_RDONLY); #endif kseq = kseq_init(fp); while (1) { my_res = qes_seqfile_read(sf, seq); kseq_res = kseq_read(kseq); tt_int_op(my_res, ==, kseq_res); if (my_res < 1 || kseq_res < 1) { /* EOF or error */ break; } tt_str_op(seq->name.str, ==, kseq->name.s); tt_str_op(seq->comment.str, ==, kseq->comment.s); tt_str_op(seq->seq.str, ==, kseq->seq.s); } end: qes_seqfile_destroy(sf); qes_seq_destroy(seq); if (kseq != NULL) kseq_destroy(kseq); if (fname != NULL) free(fname); #ifdef ZLIB_FOUND gzclose(fp); #else close(fp); #endif } /*=== FUNCTION ============================================================* Name: test_qes_seqfile_write Description: Tests the qes_seqfile_write function from qes_seqfile.c *===========================================================================*/ static void test_qes_seqfile_write (void *ptr) { struct qes_seq *seq = qes_seq_create(); size_t expt_bytes = 0; ssize_t res = 0; struct qes_seqfile *sf = NULL; char *fname = NULL; char *crc = NULL; (void) ptr; /* Make a seq to write */ qes_seq_fill_name(seq, "HWI-TEST", 8); qes_seq_fill_comment(seq, "testseq 1 2 3", 13); qes_seq_fill_seq(seq, "ACTCAATT", 8); qes_seq_fill_qual(seq, "IIIIIIII", 8); expt_bytes = 1 + 8 + 1 + 13 + 1 + /* @ + name + ' ' + comment + '\n' */ 8 + 1 + 2 + 8 + 1; /* seq + '\n' + "+\n" + qual + '\n' */ /* Test with a FASTQ seqfile */ fname = get_writable_file(); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "wT"); qes_seqfile_set_format(sf, FASTQ_FMT); res = qes_seqfile_write(sf, seq); tt_int_op(res, ==, expt_bytes); qes_seqfile_destroy(sf); /* Has to happen here to flush it */ crc = crc32_file(fname); tt_str_op(crc, ==, "d4665941"); clean_writable_file(fname); free(crc); fname = NULL; crc = NULL; /* Test with a FASTA seqfile */ expt_bytes = 1 + 8 + 1 + 13 + 1 + /* @ + name + ' ' + comment + '\n' */ 8 + 1; /* seq + '\n'*/ fname = get_writable_file(); tt_assert(fname != NULL); sf = qes_seqfile_create(fname, "wT"); qes_seqfile_set_format(sf, FASTA_FMT); /* do the write */ res = qes_seqfile_write(sf, seq); tt_int_op(res, ==, expt_bytes); qes_seqfile_destroy(sf); /* Flush it */ crc = crc32_file(fname); tt_str_op(crc, ==, "0a295c77"); clean_writable_file(fname); fname = NULL; /* Check with bad params that it returns -2 */ res = qes_seqfile_write(NULL, seq); tt_int_op(res, ==, -2); res = qes_seqfile_write(sf, NULL); tt_int_op(res, ==, -2); end: qes_seqfile_destroy(sf); qes_seq_destroy(seq); if (fname != NULL) free(fname); if (crc != NULL) free(crc); } struct testcase_t qes_seqfile_tests[] = { { "qes_seqfile_create", test_qes_seqfile_create, 0, NULL, NULL}, { "qes_seqfile_guess_format", test_qes_seqfile_guess_format, 0, NULL, NULL}, { "qes_seqfile_destroy", test_qes_seqfile_destroy, 0, NULL, NULL}, { "qes_seqfile_read_vs_kseq", test_qes_seqfile_read_vs_kseq, 0, NULL, NULL}, { "qes_seqfile_read", test_qes_seqfile_read, 0, NULL, NULL}, { "qes_seqfile_write", test_qes_seqfile_write, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_sequtil.c000066400000000000000000000041301263611052100167150ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_sequtil.c * * Description: Tests for the sequtil module * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include static void test_qes_sequtil_translate_codon (void *ptr) { size_t iii; size_t jjj; char *cdn = NULL; char aa = 0; (void) ptr; for (iii = 0; iii < n_codons; iii++) { aa = qes_sequtil_translate_codon(codon_list[iii]); tt_assert_op_type(aa, ==, aa_list[iii], char, "%c"); } tt_int_op(qes_sequtil_translate_codon("XACACA"), ==, -1); tt_int_op(qes_sequtil_translate_codon("A"), ==, -1); tt_int_op(qes_sequtil_translate_codon(NULL), ==, -1); /* Try with mutations */ for (iii = 0; iii < n_codons; iii++) { for (jjj = 0; jjj < 3; jjj++) { cdn = strdup(codon_list[iii]); cdn[jjj] = 'N'; aa = qes_sequtil_translate_codon(cdn); tt_assert_op_type(aa, ==, 'X', char, "%c"); free(cdn); cdn = NULL; } } end: if (cdn != NULL) free(cdn); } struct testcase_t qes_sequtil_tests[] = { { "qes_sequtil_translate_codon", test_qes_sequtil_translate_codon, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/test_util.c000066400000000000000000000074731263611052100162210ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: test_util.c * * Description: Test qes_util.c * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "tests.h" #include /* Actual tests */ static void test_qes_calloc(void *ptr) { void *res = NULL; const size_t bufsize = 1<<10; unsigned char *zeros[1<<10]; (void) ptr; memset(zeros, 0, bufsize); /* This should work, and the buffer should be zero throughout */ res = qes_calloc(1, 1); tt_ptr_op(res, !=, NULL); tt_int_op(memcmp(res, zeros, 1), ==, 0); free(res); res = NULL; end: if (res != NULL) free(res); } static void test_qes_malloc(void *ptr) { void *res = NULL; (void) ptr; res = qes_malloc(1); tt_ptr_op(res, !=, NULL); free(res); res = NULL; end: if (res != NULL) free(res); } static void test_qes_realloc(void *ptr) { char *res = NULL; const char *str = "test"; char *dat = strdup(str); (void) ptr; /* Test resizing buffer */ res = qes_realloc(dat, 10); dat = NULL; tt_ptr_op(res, !=, NULL); tt_int_op(memcmp(res, str, 5), ==, 0); free(res); res = NULL; end: if (res != NULL) free(res); if (dat != NULL) free(dat); } static void test_qes_free(void *ptr) { char *dat = strdup("test"); (void) ptr; /* Test freeing buffer */ tt_ptr_op(dat, !=, NULL); qes_free(dat); tt_ptr_op(dat, ==, NULL); /* This free(NULL) should not fail */ qes_free(dat); tt_ptr_op(dat, ==, NULL); end: if (dat != NULL) free(dat); } static void test_qes_roundup32 (void *ptr) { int32_t val = 3; uint32_t uval = (1u<<31) - 1; (void) ptr; /* Signed */ tt_int_op(qes_roundup32(val), ==, 4); val++; tt_int_op(qes_roundup32(val), ==, 8); val = 8; tt_int_op(qes_roundup32(val), ==, 16); val = 262143; tt_int_op(qes_roundup32(val), ==, 262144); /* Unsigned */ tt_int_op(qes_roundup32(uval), ==, 1u<<31); uval++; tt_int_op(qes_roundup32(uval), ==, 0); end: ; } static void test_qes_roundup64 (void *ptr) { int64_t val = 3; uint64_t uval = (1llu<<63) - 1; (void) ptr; /* Signed */ tt_int_op(qes_roundup64(val), ==, 4); val = 4; tt_int_op(qes_roundup64(val), ==, 8); val = 8; tt_int_op(qes_roundup64(val), ==, 16); val = 262143llu; tt_int_op(qes_roundup64(val), ==, 262144); /* Unsigned */ tt_assert(qes_roundup64(uval) == 1llu<<63); uval = 1llu<<62; tt_assert(qes_roundup64(uval) == 1llu<<63); uval = 63llu; tt_assert(qes_roundup64(uval) - 2 == 62llu); end: ; } struct testcase_t qes_util_tests[] = { { "qes_calloc", test_qes_calloc, 0, NULL, NULL}, { "qes_malloc", test_qes_malloc, 0, NULL, NULL}, { "qes_realloc", test_qes_realloc, 0, NULL, NULL}, { "qes_free", test_qes_free, 0, NULL, NULL}, { "qes_roundup32", test_qes_roundup32, 0, NULL, NULL}, { "qes_roundup64", test_qes_roundup64, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/testdata.c000066400000000000000000000126331263611052100160100ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: testdata.c * * Description: Data for tests * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #include "testdata.h" const size_t n_loremipsum_lines = 11; const size_t loremipsum_fsize = 80+76+80+75+80+79+77+75+69+1+20; const size_t loremipsum_line_lens[] = { 80, 76, 80, 75, 80, 79, 77, 75, 69, 1, 20 }; const char *loremipsum_lines[] = { "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec ornare tortor et\n", "rhoncus iaculis. Sed suscipit, arcu nec elementum vestibulum, tortor tortor\n", "dictum dui, eu sodales magna orci eu libero. Cras commodo, ligula tempor auctor\n", "vulputate, eros urna gravida eros, eget congue leo quam quis mi. Curabitur\n", "luctus augue nibh, eget vehicula augue commodo eget. Donec condimentum molestie\n", "adipiscing. In non purus lacus. Nam nec mollis mauris. Donec rhoncus, diam sit\n", "amet rhoncus viverra, lectus risus tincidunt ipsum, in dignissim justo purus\n", "eget enim. Fusce congue nulla egestas est auctor faucibus. Integer feugiat\n", "molestie leo, a interdum neque pretium nec. Etiam sit amet nibh leo.\n", "\n", "End of lorem ipsum.\n", }; const char *first_fastq_read[] = { "HWI-ST960:105:D10GVACXX:2:1101:1151:2158", "1:N:0: bcd:RPI9 seq:CACGATCAGATC", "CACGATCAGATCAANGACATTGAATCTATATGT", "JJJJJJJIJHIJCC#4ADFFHHHGHJJJJIJJJ", }; const size_t first_fastq_len = 33; const size_t n_codons = 125; const char *codon_list[] = { "AAA", "AAC", "AAG", "AAT", "AAU", "ACA", "ACC", "ACG", "ACT", "ACU", "AGA", "AGC", "AGG", "AGT", "AGU", "ATA", "ATC", "ATG", "ATT", "ATU", "AUA", "AUC", "AUG", "AUT", "AUU", "CAA", "CAC", "CAG", "CAT", "CAU", "CCA", "CCC", "CCG", "CCT", "CCU", "CGA", "CGC", "CGG", "CGT", "CGU", "CTA", "CTC", "CTG", "CTT", "CTU", "CUA", "CUC", "CUG", "CUT", "CUU", "GAA", "GAC", "GAG", "GAT", "GAU", "GCA", "GCC", "GCG", "GCT", "GCU", "GGA", "GGC", "GGG", "GGT", "GGU", "GTA", "GTC", "GTG", "GTT", "GTU", "GUA", "GUC", "GUG", "GUT", "GUU", "TAA", "TAC", "TAG", "TAT", "TAU", "TCA", "TCC", "TCG", "TCT", "TCU", "TGA", "TGC", "TGG", "TGT", "TGU", "TTA", "TTC", "TTG", "TTT", "TTU", "TUA", "TUC", "TUG", "TUT", "TUU", "UAA", "UAC", "UAG", "UAT", "UAU", "UCA", "UCC", "UCG", "UCT", "UCU", "UGA", "UGC", "UGG", "UGT", "UGU", "UTA", "UTC", "UTG", "UTT", "UTU", "UUA", "UUC", "UUG", "UUT", "UUU", }; const char aa_list[] = { 'K', 'N', 'K', 'N', 'N', 'T', 'T', 'T', 'T', 'T', 'R', 'S', 'R', 'S', 'S', 'I', 'I', 'M', 'I', 'I', 'I', 'I', 'M', 'I', 'I', 'Q', 'H', 'Q', 'H', 'H', 'P', 'P', 'P', 'P', 'P', 'R', 'R', 'R', 'R', 'R', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'E', 'D', 'E', 'D', 'D', 'A', 'A', 'A', 'A', 'A', 'G', 'G', 'G', 'G', 'G', 'V', 'V', 'V', 'V', 'V', 'V', 'V', 'V', 'V', 'V', '*', 'Y', '*', 'Y', 'Y', 'S', 'S', 'S', 'S', 'S', '*', 'C', 'W', 'C', 'C', 'L', 'F', 'L', 'F', 'F', 'L', 'F', 'L', 'F', 'F', '*', 'Y', '*', 'Y', 'Y', 'S', 'S', 'S', 'S', 'S', '*', 'C', 'W', 'C', 'C', 'L', 'F', 'L', 'F', 'F', 'L', 'F', 'L', 'F', 'F', }; void test_data_files (void *ptr) { char *fname = NULL; char *crc_res = NULL; (void) ptr; fname = find_data_file("loremipsum.txt"); crc_res = crc32_file(fname); tt_str_op(crc_res, ==, "9f20f7ec"); free(fname); free(crc_res); fname = find_data_file("loremipsum.txt.gz"); crc_res = crc32_file(fname); tt_str_op(crc_res, ==, "4e42dcb2"); free(fname); free(crc_res); fname = find_data_file("test.fastq"); crc_res = crc32_file(fname); tt_str_op(crc_res, ==, "c32cc3c0"); free(fname); free(crc_res); fname = find_data_file("test.fasta"); crc_res = crc32_file(fname); tt_str_op(crc_res, ==, "3de06bb6"); free(fname); free(crc_res); fname = find_data_file("test.fastq.gz"); crc_res = crc32_file(fname); tt_str_op(crc_res, ==, "ba1206ee"); free(fname); free(crc_res); fname = find_data_file("test.fastq.bz2"); crc_res = crc32_file(fname); tt_str_op(crc_res, ==, "c8b66d33"); end: free(fname); free(crc_res); } struct testcase_t data_tests[] = { { "data_files", test_data_files, 0, NULL, NULL}, END_OF_TESTCASES }; libqes-0.1.21/test/testdata.h000066400000000000000000000034541263611052100160160ustar00rootroot00000000000000/* * Copyright 2015 Kevin Murray * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ /* * ============================================================================ * * Filename: testdata.h * * Description: Data for tests * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef TESTDATA_H #define TESTDATA_H #include #include #include #include #include #include #include #ifndef _WIN32 #include #endif #include #include /* TinyTest */ #include "tinytest.h" #include "tinytest_macros.h" #include "testdata.h" #include "helpers.h" extern const size_t n_loremipsum_lines; extern const size_t loremipsum_fsize; extern const size_t loremipsum_line_lens[]; extern const char *loremipsum_lines[]; extern const char *first_fastq_read[]; extern const size_t first_fastq_len; extern struct testcase_t data_tests[]; extern const size_t n_codons; extern const char *codon_list[]; extern const char aa_list[]; void test_data_files (void *ptr); #endif /* TESTDATA_H */ libqes-0.1.21/test/tests.h000066400000000000000000000024651263611052100153500ustar00rootroot00000000000000/* * ============================================================================ * * Filename: tests.h * * Description: Tests for libqes * License: GPLv3+ * Author: Kevin Murray, spam@kdmurray.id.au * * ============================================================================ */ #ifndef TESTS_H #define TESTS_H #include #include #include #include #include #include #include #ifndef _WIN32 #include #endif #include #include /* TinyTest */ #include "tinytest.h" #include "tinytest_macros.h" #include "testdata.h" #include "helpers.h" #define QES_DEFAULT_ERR_FN errnil #define QES_EXIT_FN (void) #include /* test_util tests */ extern struct testcase_t qes_util_tests[]; /* test_match tests */ extern struct testcase_t qes_match_tests[]; /* test_qes_file tests */ extern struct testcase_t qes_file_tests[]; /* test_seqfile tests */ extern struct testcase_t qes_seqfile_tests[]; /* test_seq tests */ extern struct testcase_t qes_seq_tests[]; /* test_sequtil tests */ extern struct testcase_t qes_sequtil_tests[]; /* test_log tests */ extern struct testcase_t qes_log_tests[]; /* test_helpers tests */ extern struct testcase_t helper_tests[]; #endif /* TESTS_H */ libqes-0.1.21/test/tinytest/000077500000000000000000000000001263611052100157115ustar00rootroot00000000000000libqes-0.1.21/test/tinytest/tinytest.c000066400000000000000000000303711263611052100177440ustar00rootroot00000000000000/* tinytest.c -- Copyright 2009-2012 Nick Mathewson * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * 3. The name of the author may not be used to endorse or promote products * derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifdef TINYTEST_LOCAL #include "tinytest_local.h" #endif #include #include #include #include #ifndef NO_FORKING #ifdef _WIN32 #include #else #include #include #include #endif #if defined(__APPLE__) && defined(__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__) #if (__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__ >= 1060 && \ __ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__ < 1070) /* Workaround for a stupid bug in OSX 10.6 */ #define FORK_BREAKS_GCOV #include #endif #endif #endif /* !NO_FORKING */ #ifndef __GNUC__ #define __attribute__(x) #endif #include "tinytest.h" #include "tinytest_macros.h" #define LONGEST_TEST_NAME 16384 static int in_tinytest_main = 0; /**< true if we're in tinytest_main().*/ static int n_ok = 0; /**< Number of tests that have passed */ static int n_bad = 0; /**< Number of tests that have failed. */ static int n_skipped = 0; /**< Number of tests that have been skipped. */ static int opt_forked = 0; /**< True iff we're called from inside a win32 fork*/ static int opt_nofork = 0; /**< Suppress calls to fork() for debugging. */ static int opt_verbosity = 1; /**< -==quiet,0==terse,1==normal,2==verbose */ const char *verbosity_flag = ""; const struct testlist_alias_t *cfg_aliases=NULL; enum outcome { SKIP=2, OK=1, FAIL=0 }; static enum outcome cur_test_outcome = 0; const char *cur_test_prefix = NULL; /**< prefix of the current test group */ /** Name of the current test, if we haven't logged is yet. Used for --quiet */ const char *cur_test_name = NULL; #ifdef _WIN32 /* Copy of argv[0] for win32. */ static char commandname[MAX_PATH+1]; #endif static void usage(struct testgroup_t *groups, int list_groups) __attribute__((noreturn)); static int process_test_option(struct testgroup_t *groups, const char *test); static enum outcome testcase_run_bare_(const struct testcase_t *testcase) { void *env = NULL; int outcome; if (testcase->setup) { env = testcase->setup->setup_fn(testcase); if (!env) return FAIL; else if (env == (void*)TT_SKIP) return SKIP; } cur_test_outcome = OK; testcase->fn(env); outcome = cur_test_outcome; if (testcase->setup) { if (testcase->setup->cleanup_fn(testcase, env) == 0) outcome = FAIL; } return outcome; } #define MAGIC_EXITCODE 42 #ifndef NO_FORKING static enum outcome testcase_run_forked_(const struct testgroup_t *group, const struct testcase_t *testcase) { #ifdef _WIN32 /* Fork? On Win32? How primitive! We'll do what the smart kids do: we'll invoke our own exe (whose name we recall from the command line) with a command line that tells it to run just the test we want, and this time without forking. (No, threads aren't an option. The whole point of forking is to share no state between tests.) */ int ok; char buffer[LONGEST_TEST_NAME+256]; STARTUPINFOA si; PROCESS_INFORMATION info; DWORD exitcode; if (!in_tinytest_main) { printf("\nERROR. On Windows, testcase_run_forked_ must be" " called from within tinytest_main.\n"); abort(); } if (opt_verbosity>0) printf("[forking] "); snprintf(buffer, sizeof(buffer), "%s --RUNNING-FORKED %s %s%s", commandname, verbosity_flag, group->prefix, testcase->name); memset(&si, 0, sizeof(si)); memset(&info, 0, sizeof(info)); si.cb = sizeof(si); ok = CreateProcessA(commandname, buffer, NULL, NULL, 0, 0, NULL, NULL, &si, &info); if (!ok) { printf("CreateProcess failed!\n"); return 0; } WaitForSingleObject(info.hProcess, INFINITE); GetExitCodeProcess(info.hProcess, &exitcode); CloseHandle(info.hProcess); CloseHandle(info.hThread); if (exitcode == 0) return OK; else if (exitcode == MAGIC_EXITCODE) return SKIP; else return FAIL; #else int outcome_pipe[2]; pid_t pid; (void)group; if (pipe(outcome_pipe)) perror("opening pipe"); if (opt_verbosity>0) printf("[forking] "); pid = fork(); #ifdef FORK_BREAKS_GCOV vproc_transaction_begin(0); #endif if (!pid) { /* child. */ int test_r, write_r; char b[1]; close(outcome_pipe[0]); test_r = testcase_run_bare_(testcase); assert(0<=(int)test_r && (int)test_r<=2); b[0] = "NYS"[test_r]; write_r = (int)write(outcome_pipe[1], b, 1); if (write_r != 1) { perror("write outcome to pipe"); exit(1); } exit(0); return FAIL; /* unreachable */ } else { /* parent */ int status, r; char b[1]; /* Close this now, so that if the other side closes it, * our read fails. */ close(outcome_pipe[1]); r = (int)read(outcome_pipe[0], b, 1); if (r == 0) { printf("[Lost connection!] "); return 0; } else if (r != 1) { perror("read outcome from pipe"); } waitpid(pid, &status, 0); close(outcome_pipe[0]); return b[0]=='Y' ? OK : (b[0]=='S' ? SKIP : FAIL); } #endif } #endif /* !NO_FORKING */ int testcase_run_one(const struct testgroup_t *group, const struct testcase_t *testcase) { enum outcome outcome; if (testcase->flags & (TT_SKIP|TT_OFF_BY_DEFAULT)) { if (opt_verbosity>0) printf("%s%s: %s\n", group->prefix, testcase->name, (testcase->flags & TT_SKIP) ? "SKIPPED" : "DISABLED"); ++n_skipped; return SKIP; } if (opt_verbosity>0 && !opt_forked) { printf("%s%s: ", group->prefix, testcase->name); } else { if (opt_verbosity==0) printf("."); cur_test_prefix = group->prefix; cur_test_name = testcase->name; } #ifndef NO_FORKING if ((testcase->flags & TT_FORK) && !(opt_forked||opt_nofork)) { outcome = testcase_run_forked_(group, testcase); } else { #else { #endif outcome = testcase_run_bare_(testcase); } if (outcome == OK) { ++n_ok; if (opt_verbosity>0 && !opt_forked) puts(opt_verbosity==1?"OK":""); } else if (outcome == SKIP) { ++n_skipped; if (opt_verbosity>0 && !opt_forked) puts("SKIPPED"); } else { ++n_bad; if (!opt_forked) printf("\n [%s FAILED]\n", testcase->name); } if (opt_forked) { exit(outcome==OK ? 0 : (outcome==SKIP?MAGIC_EXITCODE : 1)); return 1; /* unreachable */ } else { return (int)outcome; } } int tinytest_set_flag_(struct testgroup_t *groups, const char *arg, int set, unsigned long flag) { int i, j; size_t length = LONGEST_TEST_NAME; char fullname[LONGEST_TEST_NAME]; int found=0; if (strstr(arg, "..")) length = strstr(arg,"..")-arg; for (i=0; groups[i].prefix; ++i) { for (j=0; groups[i].cases[j].name; ++j) { struct testcase_t *testcase = &groups[i].cases[j]; snprintf(fullname, sizeof(fullname), "%s%s", groups[i].prefix, testcase->name); if (!flag) { /* Hack! */ printf(" %s", fullname); if (testcase->flags & TT_OFF_BY_DEFAULT) puts(" (Off by default)"); else if (testcase->flags & TT_SKIP) puts(" (DISABLED)"); else puts(""); } if (!strncmp(fullname, arg, length)) { if (set) testcase->flags |= flag; else testcase->flags &= ~flag; ++found; } } } return found; } static void usage(struct testgroup_t *groups, int list_groups) { puts("Options are: [--verbose|--quiet|--terse] [--no-fork]"); puts(" Specify tests by name, or using a prefix ending with '..'"); puts(" To skip a test, prefix its name with a colon."); puts(" To enable a disabled test, prefix its name with a plus."); puts(" Use --list-tests for a list of tests."); if (list_groups) { puts("Known tests are:"); tinytest_set_flag_(groups, "..", 1, 0); } exit(0); } static int process_test_alias(struct testgroup_t *groups, const char *test) { int i, j, n, r; for (i=0; cfg_aliases && cfg_aliases[i].name; ++i) { if (!strcmp(cfg_aliases[i].name, test)) { n = 0; for (j = 0; cfg_aliases[i].tests[j]; ++j) { r = process_test_option(groups, cfg_aliases[i].tests[j]); if (r<0) return -1; n += r; } return n; } } printf("No such test alias as @%s!",test); return -1; } static int process_test_option(struct testgroup_t *groups, const char *test) { int flag = TT_ENABLED_; int n = 0; if (test[0] == '@') { return process_test_alias(groups, test + 1); } else if (test[0] == ':') { ++test; flag = TT_SKIP; } else if (test[0] == '+') { ++test; ++n; if (!tinytest_set_flag_(groups, test, 0, TT_OFF_BY_DEFAULT)) { printf("No such test as %s!\n", test); return -1; } } else { ++n; } if (!tinytest_set_flag_(groups, test, 1, flag)) { printf("No such test as %s!\n", test); return -1; } return n; } void tinytest_set_aliases(const struct testlist_alias_t *aliases) { cfg_aliases = aliases; } int tinytest_main(int c, const char **v, struct testgroup_t *groups) { int i, j, n=0; #ifdef _WIN32 const char *sp = strrchr(v[0], '.'); const char *extension = ""; if (!sp || stricmp(sp, ".exe")) extension = ".exe"; /* Add an exe so CreateProcess will work */ snprintf(commandname, sizeof(commandname), "%s%s", v[0], extension); commandname[MAX_PATH]='\0'; #endif for (i=1; i= 1) printf("%d tests ok. (%d skipped)\n", n_ok, n_skipped); return (n_bad == 0) ? 0 : 1; } int tinytest_get_verbosity_(void) { return opt_verbosity; } void tinytest_set_test_failed_(void) { if (opt_verbosity <= 0 && cur_test_name) { if (opt_verbosity==0) puts(""); printf("%s%s: ", cur_test_prefix, cur_test_name); cur_test_name = NULL; } cur_test_outcome = 0; } void tinytest_set_test_skipped_(void) { if (cur_test_outcome==OK) cur_test_outcome = SKIP; } char * tinytest_format_hex_(const void *val_, unsigned long len) { const unsigned char *val = val_; char *result, *cp; size_t i; if (!val) return strdup("null"); if (!(result = malloc(len*2+1))) return strdup(""); cp = result; for (i=0;i> 4]; *cp++ = "0123456789ABCDEF"[val[i] & 0x0f]; } *cp = 0; return result; } libqes-0.1.21/test/tinytest/tinytest.h000066400000000000000000000103401263611052100177430ustar00rootroot00000000000000/* tinytest.h -- Copyright 2009-2012 Nick Mathewson * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * 3. The name of the author may not be used to endorse or promote products * derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef TINYTEST_H_INCLUDED_ #define TINYTEST_H_INCLUDED_ /** Flag for a test that needs to run in a subprocess. */ #define TT_FORK (1<<0) /** Runtime flag for a test we've decided to skip. */ #define TT_SKIP (1<<1) /** Internal runtime flag for a test we've decided to run. */ #define TT_ENABLED_ (1<<2) /** Flag for a test that's off by default. */ #define TT_OFF_BY_DEFAULT (1<<3) /** If you add your own flags, make them start at this point. */ #define TT_FIRST_USER_FLAG (1<<4) typedef void (*testcase_fn)(void *); struct testcase_t; /** Functions to initialize/teardown a structure for a testcase. */ struct testcase_setup_t { /** Return a new structure for use by a given testcase. */ void *(*setup_fn)(const struct testcase_t *); /** Clean/free a structure from setup_fn. Return 1 if ok, 0 on err. */ int (*cleanup_fn)(const struct testcase_t *, void *); }; /** A single test-case that you can run. */ struct testcase_t { const char *name; /**< An identifier for this case. */ testcase_fn fn; /**< The function to run to implement this case. */ unsigned long flags; /**< Bitfield of TT_* flags. */ const struct testcase_setup_t *setup; /**< Optional setup/cleanup fns*/ void *setup_data; /**< Extra data usable by setup function */ }; #define END_OF_TESTCASES { NULL, NULL, 0, NULL, NULL } /** A group of tests that are selectable together. */ struct testgroup_t { const char *prefix; /**< Prefix to prepend to testnames. */ struct testcase_t *cases; /** Array, ending with END_OF_TESTCASES */ }; #define END_OF_GROUPS { NULL, NULL} struct testlist_alias_t { const char *name; const char **tests; }; #define END_OF_ALIASES { NULL, NULL } /** Implementation: called from a test to indicate failure, before logging. */ void tinytest_set_test_failed_(void); /** Implementation: called from a test to indicate that we're skipping. */ void tinytest_set_test_skipped_(void); /** Implementation: return 0 for quiet, 1 for normal, 2 for loud. */ int tinytest_get_verbosity_(void); /** Implementation: Set a flag on tests matching a name; returns number * of tests that matched. */ int tinytest_set_flag_(struct testgroup_t *, const char *, int set, unsigned long); /** Implementation: Put a chunk of memory into hex. */ char *tinytest_format_hex_(const void *, unsigned long); /** Set all tests in 'groups' matching the name 'named' to be skipped. */ #define tinytest_skip(groups, named) \ tinytest_set_flag_(groups, named, 1, TT_SKIP) /** Run a single testcase in a single group. */ int testcase_run_one(const struct testgroup_t *,const struct testcase_t *); void tinytest_set_aliases(const struct testlist_alias_t *aliases); /** Run a set of testcases from an END_OF_GROUPS-terminated array of groups, as selected from the command line. */ int tinytest_main(int argc, const char **argv, struct testgroup_t *groups); #endif libqes-0.1.21/test/tinytest/tinytest_macros.h000066400000000000000000000160361263611052100213170ustar00rootroot00000000000000/* tinytest_macros.h -- Copyright 2009-2012 Nick Mathewson * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * 3. The name of the author may not be used to endorse or promote products * derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef TINYTEST_MACROS_H_INCLUDED_ #define TINYTEST_MACROS_H_INCLUDED_ /* Helpers for defining statement-like macros */ #define TT_STMT_BEGIN do { #define TT_STMT_END } while (0) /* Redefine this if your test functions want to abort with something besides * "goto end;" */ #ifndef TT_EXIT_TEST_FUNCTION #define TT_EXIT_TEST_FUNCTION TT_STMT_BEGIN goto end; TT_STMT_END #endif /* Redefine this if you want to note success/failure in some different way. */ #ifndef TT_DECLARE #define TT_DECLARE(prefix, args) \ TT_STMT_BEGIN \ printf("\n %s %s:%d: ",prefix,__FILE__,__LINE__); \ printf args ; \ TT_STMT_END #endif /* Announce a failure. Args are parenthesized printf args. */ #define TT_GRIPE(args) TT_DECLARE("FAIL", args) /* Announce a non-failure if we're verbose. */ #define TT_BLATHER(args) \ TT_STMT_BEGIN \ if (tinytest_get_verbosity_()>1) TT_DECLARE(" OK", args); \ TT_STMT_END #define TT_DIE(args) \ TT_STMT_BEGIN \ tinytest_set_test_failed_(); \ TT_GRIPE(args); \ TT_EXIT_TEST_FUNCTION; \ TT_STMT_END #define TT_FAIL(args) \ TT_STMT_BEGIN \ tinytest_set_test_failed_(); \ TT_GRIPE(args); \ TT_STMT_END /* Fail and abort the current test for the reason in msg */ #define tt_abort_printf(msg) TT_DIE(msg) #define tt_abort_perror(op) TT_DIE(("%s: %s [%d]",(op),strerror(errno), errno)) #define tt_abort_msg(msg) TT_DIE(("%s", msg)) #define tt_abort() TT_DIE(("%s", "(Failed.)")) /* Fail but do not abort the current test for the reason in msg. */ #define tt_failprint_f(msg) TT_FAIL(msg) #define tt_fail_perror(op) TT_FAIL(("%s: %s [%d]",(op),strerror(errno), errno)) #define tt_fail_msg(msg) TT_FAIL(("%s", msg)) #define tt_fail() TT_FAIL(("%s", "(Failed.)")) /* End the current test, and indicate we are skipping it. */ #define tt_skip() \ TT_STMT_BEGIN \ tinytest_set_test_skipped_(); \ TT_EXIT_TEST_FUNCTION; \ TT_STMT_END #define tt_want_(b, msg, fail) \ TT_STMT_BEGIN \ if (!(b)) { \ tinytest_set_test_failed_(); \ TT_GRIPE(("%s",msg)); \ fail; \ } else { \ TT_BLATHER(("%s",msg)); \ } \ TT_STMT_END /* Assert b, but do not stop the test if b fails. Log msg on failure. */ #define tt_want_msg(b, msg) \ tt_want_(b, msg, ); /* Assert b and stop the test if b fails. Log msg on failure. */ #define tt_assert_msg(b, msg) \ tt_want_(b, msg, TT_EXIT_TEST_FUNCTION); /* Assert b, but do not stop the test if b fails. */ #define tt_want(b) tt_want_msg( (b), "want("#b")") /* Assert b, and stop the test if b fails. */ #define tt_assert(b) tt_assert_msg((b), "assert("#b")") #define tt_assert_test_fmt_type(a,b,str_test,type,test,printf_type,printf_fmt, \ setup_block,cleanup_block,die_on_fail) \ TT_STMT_BEGIN \ type val1_ = (a); \ type val2_ = (b); \ int tt_status_ = (test); \ if (!tt_status_ || tinytest_get_verbosity_()>1) { \ printf_type print_; \ printf_type print1_; \ printf_type print2_; \ type value_ = val1_; \ setup_block; \ print1_ = print_; \ value_ = val2_; \ setup_block; \ print2_ = print_; \ TT_DECLARE(tt_status_?" OK":"FAIL", \ ("assert(%s): "printf_fmt" vs "printf_fmt, \ str_test, print1_, print2_)); \ print_ = print1_; \ cleanup_block; \ print_ = print2_; \ cleanup_block; \ if (!tt_status_) { \ tinytest_set_test_failed_(); \ die_on_fail ; \ } \ } \ TT_STMT_END #define tt_assert_test_type(a,b,str_test,type,test,fmt,die_on_fail) \ tt_assert_test_fmt_type(a,b,str_test,type,test,type,fmt, \ {print_=value_;},{},die_on_fail) #define tt_assert_test_type_opt(a,b,str_test,type,test,fmt,die_on_fail) \ tt_assert_test_fmt_type(a,b,str_test,type,test,type,fmt, \ {print_=value_?value_:"";},{},die_on_fail) /* Helper: assert that a op b, when cast to type. Format the values with * printf format fmt on failure. */ #define tt_assert_op_type(a,op,b,type,fmt) \ tt_assert_test_type(a,b,#a" "#op" "#b,type,(val1_ op val2_),fmt, \ TT_EXIT_TEST_FUNCTION) #define tt_int_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,long,(val1_ op val2_), \ "%ld",TT_EXIT_TEST_FUNCTION) #define tt_uint_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,unsigned long, \ (val1_ op val2_),"%lu",TT_EXIT_TEST_FUNCTION) #define tt_ptr_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,const void*, \ (val1_ op val2_),"%p",TT_EXIT_TEST_FUNCTION) #define tt_str_op(a,op,b) \ tt_assert_test_type_opt(a,b,#a" "#op" "#b,const char *, \ (val1_ && val2_ && strcmp(val1_,val2_) op 0),"<%s>", \ TT_EXIT_TEST_FUNCTION) #define tt_mem_op(expr1, op, expr2, len) \ tt_assert_test_fmt_type(expr1,expr2,#expr1" "#op" "#expr2, \ const void *, \ (val1_ && val2_ && memcmp(val1_, val2_, len) op 0), \ char *, "%s", \ { print_ = tinytest_format_hex_(value_, (len)); }, \ { if (print_) free(print_); }, \ TT_EXIT_TEST_FUNCTION \ ); #define tt_want_int_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,long,(val1_ op val2_),"%ld",(void)0) #define tt_want_uint_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,unsigned long, \ (val1_ op val2_),"%lu",(void)0) #define tt_want_ptr_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,const void*, \ (val1_ op val2_),"%p",(void)0) #define tt_want_str_op(a,op,b) \ tt_assert_test_type(a,b,#a" "#op" "#b,const char *, \ (strcmp(val1_,val2_) op 0),"<%s>",(void)0) #endif libqes-0.1.21/util/000077500000000000000000000000001263611052100140245ustar00rootroot00000000000000libqes-0.1.21/util/make_codon_list.py000066400000000000000000000014271263611052100175340ustar00rootroot00000000000000from Bio.Data import CodonTable nts = "ACGTU" codons = [] aas = [] codon_tab = CodonTable.generic_by_name["Standard"].forward_table for a in nts: for b in nts: for c in nts: codon = "".join((a,b,c)) try: aa = codon_tab[codon.replace("U", "T")] except KeyError: aa = "*" codons.append(codon) aas.append(aa) n = 0 print "const size_t n_codons = %s;" % len(codons) print print "const char *codon_list[] = {" , for cdn in codons: if n % 5 == 0: print "\n ", print '"%s", ' % cdn, n += 1 print print "};" n = 0 print print "const char aa_list[] = {", for aa in aas: if n % 5 == 0: print "\n ", print "'%s', " % aa, n += 1 print print "};" print libqes-0.1.21/util/make_codon_map.py000066400000000000000000000011561263611052100173350ustar00rootroot00000000000000from Bio.Data import CodonTable nts = "ACGTU" codon_tab = CodonTable.generic_by_name["Standard"].forward_table print "char\ntranslate_codon(char *codon)\n{" for a in nts: print " else if (codon[0] == '%s') {" % a for b in nts: print " else if (codon[1] == '%s') {" % b for c in nts: print " else if (codon[2] == '%s')" % c , codon = "".join((a,b,c)) try: aa = codon_tab[codon] except KeyError: aa = "*" print "return '%s'" % aa print " }" print " }" print "}"