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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%
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ebanks 5a20bf0e64 3 changes to UG which break integration tests: 
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-09 17:16:47 +00:00
R PlotDepthOfCoverage now produces a set of useful QC plots. Currently a first-draft, and it is unclear how the visualization will scale with increasing sample size and/or depth. 2010-03-09 16:42:35 +00:00
archive moving older versions of the oneoff project to archive, bye-bye 2010-02-04 19:46:27 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java 3 changes to UG which break integration tests: 2010-03-09 17:16:47 +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 removing the package description for the VCF validator 2010-03-02 15:45:51 +00:00
perl Band-Aid: changed the pointers from mike's home directory to a checkout of the last know working revision r7169 in my directory. 2010-03-07 04:19:01 +00:00
python Make annotated VCF not be broken 2010-03-01 23:22:41 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala/src Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 2009-11-02 06:02:41 +00:00
settings adding a stripped down Tribble library for the start of integration 2010-02-17 21:29:25 +00:00
shell Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 2009-09-04 12:39:06 +00:00
testdata a small dbsnp file for Tribble testing 2010-02-18 18:12:55 +00:00
build.xml In the new sharding system, if no read group is present, hallucinate one. Added 2010-03-07 23:01:34 +00:00
ivy.xml adding a stripped down Tribble library for the start of integration 2010-02-17 21:29:25 +00:00