Reapr_1.0.18/ 0000755 0030556 0002036 00000000000 12472631102 011366 5 ustar mh12 team81 Reapr_1.0.18/changelog.txt 0000644 0030556 0002036 00000012407 12472630745 014076 0 ustar mh12 team81 ______ 1.0.17 -> 1.0.18 ______
* Bug fix for rare cases when sampling to get coverage/GC sstats.
* When writing broken assembly, no by default include all bin
contigs >= 1000 bases long in the main assembly. Can change this
cutoff with -m option. Short contigs still written to the bin.
______ 1.0.16 -> 1.0.17 ______
* Expose number of threads option in smalt map
* Expose all task options when running the pipeline
* Bug fix with some options not working in stats task.
* Add comma to the list of bad characters in facheck
* Update manual to reflect changes and change examples
to have what to do with just one library. Fix a couple
of typos in examples.
* Speed up fa2gc stage of preprocess by about 4 times.
______ 1.0.15 -> 1.0.16 ______
* Added option -t to task 'break'. This can be used to trim
bases off contigs ends, wherever a contig is broken from an
FCD error with the -a option.
* Change default of -l option of break to output sequences that are at
least 100bp long (default was 1bp).
* install.sh now checks that the required Perl modules are installed, and
checks that R is in the path.
* install.sh checks that the OS appears to be Linux and dies if
it's not. Added option to try to force the install anyway regardless of OS.
* Bug fix in smaltmap: depending on the OS, bam header was not getting
made correctly.
* smaltmap now starts by running samtools faidx on the assembly fasta file.
A common cause of the pipeline falling over is a fasta file that makes
samtools faidx segfault. Print a nice error message about this
if samtools faidx ends badly.
______ 1.0.14 -> 1.0.15 ______
* Added task 'seqrename' to rename all the sequences
in a BAM file. This saves remapping the reads to make a
new BAM that will be OK for the pipeline.
* Added task 'smaltmap' run map reads using SMALT.
* Updated the plots task to make tabix indexed plots, since
Artemis (version 15.0.0) can now read these.
* Bug fix in task 'break', where the -l option for min length
of sequence to output didn't always work.
______ 1.0.13 -> 1.0.14 ______
* Fixed Makefiles for tabix and reapr because they didn't work
on some systems (e.g. Ubuntu).
* Change sequence names output by break: use underscores instead
of : and -, so that the output is compatible with REAPR itself.
* Added -b option to break, which will ignore FCD and low fragment
coverage errors within contigs (i.e. those that don't contain a
gap)
______ 1.0.12 -> 1.0.13 ______
* Bug fix: off by one error in coordinates in
errors gff file made by 'score'.
* pipeline now starts by running facheck
on the assembly.
* pipeline changed so that it writes a bash
script of all the commands it's going to run,
then runs that bash script. Useful if it dies
and you want to know the commands needed to finish
the pipeline.
* Change in perfectmap: added --variance to be
0.5 * fragment size in the call to snpomatic.
The previous default was 0.25 * fragment size.
* Added -a option to 'break' for aggressive breaking:
it breaks contigs at errors (as well as breaking at
gaps).
______ 1.0.11 -> 1.0.12 ______
* Bug fix where in rare cases the 'break'
task would incorrectly make a broken fasta file
with duplicated sequences, or sequences continuing
right through to the end of the scaffold, instead of
stopping at the appropriate gap.
* Prefix the name of every bin contig
made when running break with 'REAPR_bin.'.
* In facheck, added brackets (){} and various
other characters to the list of characters that
break the pipeline.
* More verbose error message in preprocess when
something goes wrong at the point of sampling the
fragment coverage vs GC content.
* Fix typo in report.txt file made by summary, should be
'low score' not 'high score'. Also now writes the same
information in a report.tsv file, for ease of putting
results into spreadsheets.
______ 1.0.10 -> 1.0.11 ______
* Switch meaning of score to be more intuitive,
so that a score of 1 means perfect, down to
0 for bad. Give all gaps a score of -1.
______ 1.0.9 -> 1.0.10 ______
* Bug fix with counting perfect bases. It was slightly
overestimating, by counting gaps which were too long
to call as perfect.
______ 1.0.8 -> 1.0.9 ______
* Added task 'perfectfrombam' to use as an alternative to
perfectmap. perfectmap maps reads with SNP-o-matic, which
is very fast but also very high memory. perfectmapfrombam
takes a BAM file as input, and generates a file of perfect
and uniquely mapped reads, same format as for perfectmap,
for use in the REAPR pipeline. Intended use case is
large genomes.
* Fix bug where facheck was writing .fa and .info files
when just an assembly fasta was given as input, with no
output files prefix.
* Bug fix of link reporting. The coords needed 1 adding
to them in the Note... section of the gff file made by score.
* Remove superfluous double-quotes in the note section
of the gff errors file made by score.
* For each plot file, now additionally writes data in a .dat file,
(the R plots truncate the x axis and so the .R files don't
have all the data in them, but the .dat files do
have all the data in them, should anyone want it).
* Add option -u to stats task, to just run on a given
list of chromosomes.
* Added -f to every system call to tabix
* 'break' now also outputs a prefix.broken_assembly_bin.fa
fasta file of the parts of the genomes which were replaced
with Ns.
Reapr_1.0.18/install.sh 0000755 0030556 0002036 00000010404 12472630745 013406 0 ustar mh12 team81 #!/usr/bin/env bash
set -e
rootdir=$PWD
unamestr=$(uname)
# Check if the OS seems to be Linux. This should be informative to
# Windows/Mac users that are trying to install this, despite it being
# developed for Linux. There is a VM avilable for Mac/Windows.
if [ "$unamestr" != "Linux" ]
then
echo "Operating system does not appear to be Linux: uname says it's '$unamestr'"
if [ "$1" = "force" ]
then
echo "'force' option used, carrying on anyway. Best of luck to you..."
else
echo "
If you *really* want to try installing anyway, run this:
./install.sh force
If you're using a Mac or Windows, then the recommended way to run REAPR is
to use the virtual machine."
exit 1
fi
fi
echo "------------------------------------------------------------------------------
Checking prerequisites
------------------------------------------------------------------------------
"
echo "Checking Perl modules..."
modules_ok=1
for module in File::Basename File::Copy File::Spec File::Spec::Link Getopt::Long List::Util
do
set +e
perl -M$module -e 1 2>/dev/null
if [ $? -eq 0 ]
then
echo " OK $module"
else
echo " NOT FOUND: $module"
modules_ok=0
fi
set -e
done
if [ $modules_ok -ne 1 ]
then
echo "Some Perl modules were not found - please install them. Cannot continue"
exit 1
else
echo "... Perl modules all OK"
fi
echo
echo "Looking for R..."
if type -P R
then
echo "... found R OK"
else
echo "Didn't find R. It needs to be installed and in your path. Cannot continue"
fi
cd third_party
echo "
------------------------------------------------------------------------------
Compiling cmake
------------------------------------------------------------------------------
"
cd cmake
./bootstrap --prefix $PWD
make
cd ..
echo "
------------------------------------------------------------------------------
cmake compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling Bamtools
------------------------------------------------------------------------------
"
cd bamtools
mkdir build
cd build
$rootdir/third_party/cmake/bin/cmake ..
make
cd $rootdir
echo "
------------------------------------------------------------------------------
Bamtools compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling Tabix
------------------------------------------------------------------------------
"
cd third_party/tabix
make
cd ..
echo "
------------------------------------------------------------------------------
Tabix compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling snpomatic
------------------------------------------------------------------------------
"
cd snpomatic
make
cd ..
echo "
------------------------------------------------------------------------------
snpomatic compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling samtools
------------------------------------------------------------------------------
"
cd samtools
make
echo "
------------------------------------------------------------------------------
samtools compiled
------------------------------------------------------------------------------
"
echo "
------------------------------------------------------------------------------
Compiling Reapr
------------------------------------------------------------------------------
"
cd $rootdir/src
make
cd ..
ln -s src/reapr.pl reapr
echo "
Reapr compiled
All done!
Run
./reapr
for usage.
Read the manual
manual.pdf
for full instructions
"
Reapr_1.0.18/licence.txt 0000644 0030556 0002036 00000104513 12472630745 013551 0 ustar mh12 team81 GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
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Also add information on how to contact you by electronic and paper mail.
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The hypothetical commands `show w' and `show c' should show the appropriate
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For more information on this, and how to apply and follow the GNU GPL, see
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The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
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the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
.
Reapr_1.0.18/README 0000644 0030556 0002036 00000005446 12472630745 012273 0 ustar mh12 team81 REAPR version 1.0.18 README file
_____________________________ INSTALLATION ___________________________________
Prerequisites:
- R installed and in your path (http://www.r-project.org/)
- The following Perl modules need to be installed:
File::Basename
File::Copy
File::Spec
File::Spec::Link
Getopt::Long
List::Util
To install REAPR, run
./install.sh
Note that (depending on your system) this could take quite a long time
because there are several third-party tools that need to be compiled.
Once it has finished, add ./reapr to your $PATH, or call it explicitly with
/path/to/your/installation/directory/reapr
Optionally, you might want to have Artemis installed
(http://www.sanger.ac.uk/resources/software/artemis/) to view the output.
It must be at least Artemis version 15.0.0.
______________________________ RUN THE TEST __________________________________
If you want to check the installation is ok, you can run a test of the
whole REAPR pipeline.
IMPORTANT: the test assumes that 'reapr' has been added to your $PATH.
The test data are available as a separate download. These are solely to check
that the installation runs, using a cut-down dataset. As such, the results
are not the same as those that would be obtained when running on the full
dataset. The data contains reads from the ENA (accession number SRR022865).
The remainder of the test data is from the GAGE paper
(Salzberg et al. 2011), using the Velvet assembly of S. aureus
(see http://gage.cbcb.umd.edu/data/index.html).
Download the test data tarball, unpack it and run the
test script from inside the test directory:
./test.sh
____________________________ MAPPING READS ___________________________________
SMALT (http://www.sanger.ac.uk/resources/software/smalt/) is recommended to
map the reads. REAPR has been tested using versions 0.6.4 and 0.7.0.1 of
SMALT, but we have noticed issues with writing a BAM file directly
(with the SMALT option -f bam). Please use -f samsoft when running SMALT, then
import to BAM with samtools or Picard.
REAPR can map reads for you using SMALT - you can run 'reapr smaltmap' with
the -x option to print a list of the mapping commands that REAPR would
run to produce a BAM for input to the REAPR pipeline.
________________________________ GET HELP ____________________________________
Please read the manual: manual.pdf
_______________________________ BRIEF USAGE __________________________________
All REAPR tasks are run via a call to
reapr
Call with no arguments for a list of tasks. Call any task with no arguments
to get the usage for that task. To run the entire pipeline, run
reapr pipeline
Full instructions can be found in the manual: manual.pdf.
__________________________ BUG REPORTS/QUESTIONS/COMMENTS ____________________
Please email Martin Hunt, mh12@sanger.ac.uk.
Reapr_1.0.18/src/ 0000755 0030556 0002036 00000000000 12472630755 012172 5 ustar mh12 team81 Reapr_1.0.18/src/bam2fragCov.cpp 0000644 0030556 0002036 00000013613 12310266322 015015 0 ustar mh12 team81 #include
#include
#include
#include
#include
#include
#include