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R.methodsS3 adding R libraries
R.oo adding R libraries
cloud
cmdline Added dependency checking, .gitignore
dependencies Delete stampy-latest.tgz
example
example_MSG_toy
instructions
tests Ignore changes in non-deterministic output files when testing.
tools
.gitignore
README
TQSfastq.py
Utils.pm
barcode_splitter.py
breakpoint-widths.R First commit
combine.py
countalleles.c
create_stats.py
ded.R
extract-ref-alleles.py Improved memory handling
fastq_2_fasta.pl
filter-sam.py Brought over Tina hu's changes to be compatible with later versions o…
fit-hmm.R Only output ests, and CSV files when pepthresh is set. (to save disc …
grepfqparser.py
hmmlib.R
hmmprob_to_est.py Added another row to file format, added memory and time tracking
hmmprobs.c
make-pileups.sh Make grep call compatible across Linux versions
makefile
mapping_functions.py
msg.pl
msgCluster.pl several features: fix msg.chrlength, max_read_length, parameter for c…
msgUpdateParentals.pl
msglib.py
parent1or2-hmm.sh
parse_BCdata2BWA.pl Added new parsing option, updated validation of parents in update par…
parse_and_map.py
plot_error.R
print_dependencies.sh
reformatFasta4sam.pl
send_email.py Changes to print dependencies, Changes to email when complete
summaryPlots.R fixed chrom printing
summary_mismatch.pl Fixed issue where newlines were being included in barcode names when …
test_dependencies.sh Test dependencies before running MSG
test_dependencies_R.R
test_dependencies_R.sh
test_dependencies_executable.sh
test_dependencies_perl.pl
test_dependencies_python.py
updateRef.pl first attempt at making trimming and updating updating parents steps …
validate.py
version
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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