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R.methodsS3 adding R libraries
R.oo
cloud Update StarCluster_notes.txt
cmdline Added dependency checking, .gitignore
dependencies Delete stampy-latest.tgz
example Added difffac parameter to msg.cfg file
example_MSG_toy Update msg.cfg
instructions misc
tests Ignore changes in non-deterministic output files when testing.
tools Update DisambiguateGenomes.py
.gitignore updated ignore file for testing
README several features: fix msg.chrlength, max_read_length, parameter for c…
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Utils.pm Update Utils.pm
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countalleles.c First commit
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grepfqparser.py Pre-unzip reads file for new parser. Update how parsing stats are cre…
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msg.pl several features: fix msg.chrlength, max_read_length, parameter for c…
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msgUpdateParentals.pl Added new custom qsub option in config files to be used in ALL qsub c…
msglib.py Changed extract ref alleles to dynamically determine how much system …
parent1or2-hmm.sh several features: fix msg.chrlength, max_read_length, parameter for c…
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test_dependencies.sh Test dependencies before running MSG
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test_dependencies_R.sh Added dependency checking, .gitignore
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test_dependencies_perl.pl Test dependencies before running MSG
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version several features: fix msg.chrlength, max_read_length, parameter for c…
write-hmm-data.R Fixing grep call

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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