gatk3的最后一个经典版本3.8

chartl be31d7f4cc Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it. ... This will output for hapmap variant sites: chromosome position ref allele variant allele number of variant alleles of the individuals depth of coverage power to detect singletons at lod 3 number of variant bases seen whether or not variant was called git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 15:47:52 +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	Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it.	2009-11-18 15:47:52 +00:00
packages	Extract and include only the Tim Fennell-approved parts of picard private.	2009-11-13 19:42:33 +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	Extract and include only the Tim Fennell-approved parts of picard private.	2009-11-13 19:42:33 +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