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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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carneiro 0048f1f6d3 Lots of interval_list file utility scripts 
1. findGenes : Parses the Genetic Association Database (from NIH) into an annotated 'genes of interest' interval_list file.
 
2. sortGenesByCoverage : combines the interval_list of the genes of interest with the report from GATK's DepthOfCoverage, generating an annotated interval_list with total and average coverages on each gene.
  
3. hasTheseTargets : Give it a list of targets (example: exon targets) and any interval_list (example: genes of interest) and it will generate an annotated interval_list of all the exons that are contained in the list of genes. 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5894 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-05-27 18:31:07 +00:00
R Utitlity function to for plotting post-run qc metrics 2011-05-26 20:14:25 +00:00
analysis/depristo CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself. 2011-05-21 14:02:30 +00:00
archive Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway 2011-05-22 18:43:48 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +00:00
chainFiles Renamed for consistency 2011-05-25 02:12:21 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java misc cleanup 2011-05-27 16:49:20 +00:00
lua Lots of interval_list file utility scripts 2011-05-27 18:31:07 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Added cofoja to the Queue package. Although BCEL doesn't think they're needed the scala compiler respectfully disagrees. 2011-05-26 17:42:34 +00:00
perl Quit immediately with an error message if any of the individual steps fails. 2011-04-22 13:23:33 +00:00
python A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles) 2011-03-21 16:11:55 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala removing dependance on jobQueue == gsa 2011-05-27 10:12:09 +00:00
settings Contracts for Java (http://code.google.com/p/cofoja/) infrastructure enabled. No piece of code actually uses this, so it's possible to remove easily. Does not build by default (you must modify build.xml). Really an intermediate commit so I can play around with the system in my java classes and revert safely. Very much looking forward to DVCS 2011-05-18 18:05:59 +00:00
shell Useful utility for looking at the file size of GSA file systems 2011-04-02 03:47:27 +00:00
testdata Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting 2011-05-04 13:56:01 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Build for tests now includes path to contracts 2011-05-22 19:44:49 +00:00
ivy.xml Factor out all testing dependencies into a separate test configuration and 2011-05-05 22:42:11 +00:00