gatk3的最后一个经典版本3.8

ebanks e9a8156cfb Use new optimized ReadBackedPileup ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2184 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-30 18:17:18 +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	Add a Unix-standard version number to the file.	2009-11-23 20:07:17 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Use new optimized ReadBackedPileup	2009-11-30 18:17:18 +00:00
matlab	A new subversion repository for matlab scripts, so they don't go away in case of catastrophic Yang failure.	2009-11-30 16:25:07 +00:00
packages	Add IlluminaUtil to picard-private.jar	2009-11-25 19:25:21 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Better support for comparison to truth. Now emits FP rates for each covariate if a truth file is provided. Also now writes out a detailed recal.log file that can be parsed directly into R	2009-11-29 22:20:40 +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	Push version number of picard-private-parts	2009-11-25 19:28:57 +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	New VariantFiltration.	2009-11-20 19:50:26 +00:00