gatk3的最后一个经典版本3.8

hanna ee2ec7ced9 Fix off-by-one error in original implementation of read sharding. Tested by ... awking output of BamToFastq vs. samtools until the outputs matched exactly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-06 18:52:53 +00:00
R	Using bitmap() instead of png() since the former doesn't rely on X11.	2010-02-23 05:31:51 +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	Fix off-by-one error in original implementation of read sharding. Tested by	2010-03-06 18:52:53 +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	Allow no-call alleles to propagate through to the MAF file	2010-02-16 20:46:16 +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	Sharding system fixes for corner cases generally related to lack of coverage	2010-03-04 18:59:21 +00:00
ivy.xml	adding a stripped down Tribble library for the start of integration	2010-02-17 21:29:25 +00:00