gatk-3.8

gatk3的最后一个经典版本3.8

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depristo 44ea55d338 Useful library for parsing VCF files, plus a general VCF->table converter git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1964 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-03 13:14:04 +00:00
R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00
c	The BWA/C bindings were triggering the local aligner to repeatedly reload the	2009-11-03 00:01:55 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	improvements to VCF and variant eval support of VCF -- now listens to the filter field	2009-11-03 12:09:30 +00:00
packages	added IndelGenotyperV2Walker	2009-10-29 20:07:31 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Useful library for parsing VCF files, plus a general VCF->table converter	2009-11-03 13:14:04 +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	Bumping version of Picard for firehose compatibility.	2009-10-16 19:38:56 +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	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	Restore a jar packaging change that got clobbered.	2009-11-03 00:15:45 +00:00
ivy.xml	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