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Latest commit 2a45785 Mar 8, 2016 @YourePrettyGood YourePrettyGood committed with gregpinero Added handling of haplodiploid species
MSG should now be able to handle haplodiploid species, since we can now
specify all scaffolds as being sex chromosomes (sexchroms=all).
Remember to specify the haploid sex as "male" in the barcodes file, and
the diploid sex as "female".

Signed-off-by: Greg Pinero <gregpinero@gmail.com>
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R.methodsS3 adding R libraries Apr 6, 2011
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cloud Update StarCluster_notes.txt Oct 9, 2014
cmdline Added dependency checking, .gitignore Jun 6, 2011
dependencies Delete stampy-latest.tgz Sep 30, 2014
example Added difffac parameter to msg.cfg file Jan 28, 2015
example_MSG_toy Update msg.cfg Sep 10, 2014
instructions Updated cloud instructions to help with common issues and be clearer Feb 19, 2016
tests Ignore changes in non-deterministic output files when testing. Oct 24, 2011
tools Update DisambiguateGenomes.py Sep 9, 2014
.gitignore updated ignore file for testing Sep 6, 2011
README several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
TQSfastq.py Changes for new mapping algorithms Mar 13, 2012
Utils.pm Update Utils.pm Sep 29, 2014
barcode_splitter.py Made compressed files compatible with illumina index parsing Jun 1, 2012
breakpoint-widths.R First commit Apr 6, 2011
combine.py several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
countalleles.c First commit Apr 6, 2011
create_stats.py Pre-unzip reads file for new parser. Update how parsing stats are cre… Oct 25, 2013
ded.R
extract-ref-alleles.py Improved memory handling Mar 24, 2014
fastq_2_fasta.pl adding fastq_2_fasta file Apr 6, 2011
filter-sam.py Brought over Tina hu's changes to be compatible with later versions o… Apr 4, 2012
fit-hmm.R Added handling of haplodiploid species Apr 8, 2016
grepfqparser.py Pre-unzip reads file for new parser. Update how parsing stats are cre… Oct 25, 2013
hmmlib.R revert accidental commit Oct 30, 2013
hmmprob_to_est.py Added another row to file format, added memory and time tracking Mar 4, 2014
hmmprobs.c revert accidental commit Oct 30, 2013
make-pileups.sh Make grep call compatible across Linux versions Oct 2, 2014
makefile First commit Apr 6, 2011
mapping_functions.py Don't overwrite stats file on reruns Oct 30, 2013
msg.pl several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
msgCluster.pl several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
msgUpdateParentals.pl
msglib.py Changed extract ref alleles to dynamically determine how much system … Dec 14, 2011
parent1or2-hmm.sh several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
parse_BCdata2BWA.pl Added new parsing option, updated validation of parents in update par… Feb 21, 2013
parse_and_map.py Always quality trim files if requested even when already parsed Jul 30, 2015
plot_error.R
print_dependencies.sh more dependency printing Oct 15, 2013
reformatFasta4sam.pl Finished changes to accept gzipped input (but backed out changes to c… May 23, 2012
send_email.py
summaryPlots.R fixed chrom printing May 19, 2011
summary_mismatch.pl Fixed issue where newlines were being included in barcode names when … Apr 17, 2012
test_dependencies.sh Test dependencies before running MSG Jun 13, 2012
test_dependencies_R.R Added dependency checking, .gitignore Jun 6, 2011
test_dependencies_R.sh Added dependency checking, .gitignore Jun 6, 2011
test_dependencies_executable.sh Fixed how dep. script checks Python version, updated README to point … Sep 8, 2011
test_dependencies_perl.pl Test dependencies before running MSG Jun 13, 2012
test_dependencies_python.py Added dependency checking, .gitignore Jun 6, 2011
updateRef.pl first attempt at making trimming and updating updating parents steps … May 22, 2012
validate.py several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
version Update version Sep 22, 2015
write-hmm-data.R Fixing grep call Oct 3, 2014

README

MSG: Multiplexed Shotgun Genotyping
http://genomics.princeton.edu/AndolfattoLab/MSG.html
https://github.com/JaneliaSciComp/msg
http://www.ncbi.nlm.nih.gov/pubmed/21233398

### Dependencies ###
Run test_dependencies.sh to check for the existence of dependencies

NOTE: Most of these packages can be found in the dependencies directory for you to 
extract and install as needed on your system.

Python (2.6.4)
numpy (recent versions should be fine)
bwa (0.5.7)
samtools (0.1.9-3)  ! Newer versions of Samtools will not work !
biopython-1.53
Pyrex-0.9.9
pysam-0.1.2 (apply fix as described here: http://code.google.com/p/pysam/issues/detail?id=22&can=1&q=dandavison0)
R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3)
Perl Modules (IO::Uncompress::Gunzip)
    -- A command like this should work on Unix Desktop Systems:
    -- perl -MCPAN -e 'install IO::Uncompress::Gunzip'
mailer (Python package: http://pypi.python.org/pypi/mailer) - optional; for sending email alert when run completes

### Installation instructions ###
git clone git://github.com/JaneliaSciComp/msg.git
cd msg
make

### Toy Example ###
The toy example is useful to check that MSG and dependencies are installed and functioning correctly.
TODO

### Example with Real Data ###
Download the data from NCBI's Sequence Read Archive and MSG config and barcodes file
 - example/get_sample_data.sh (requires wget)

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