gatk-3.8

gatk3的最后一个经典版本3.8

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alecw 4082f4677e Picard-private with classes for reading Picard dbSNP binary file git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2086 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-19 17:24:28 +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	Bulletproofing code. If errors are encountering during the run, turn them	2009-11-14 22:57:16 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Test to ensure that ConcordanceTruthTable and those walkers which rely on it for tabulating pooled truth information from truth information of the individuals within the pool is doing that calculation correctly. Tests single het, single hom (with/without reference), together, together without reference, and a mix of everything.	2009-11-19 15:26:32 +00:00
packages	Picard-private with classes for reading Picard dbSNP binary file	2009-11-19 17:24:28 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	cleanup of SNP selector -- ready for some additional testing	2009-11-13 21:46:31 +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	Picard-private with classes for reading Picard dbSNP binary file	2009-11-19 17:24:28 +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	Build aligner as separate jar file.	2009-11-13 22:29:29 +00:00
ivy.xml	Extract and include only the Tim Fennell-approved parts of picard private.	2009-11-13 19:42:33 +00:00