gatk3的最后一个经典版本3.8

aaron ac2a207b0b added a wrapper exception for anything that goes wrong in VCF parsing; this way the problematic file line is emitted, no matter what happens. Makes debugging a lot easier, especially in large files. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2739 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-29 19:58:51 +00:00
R	AnalyzeAnnotations now breaks out titv by calls in hapmap and also plots true positive rates. Any RODs passed in whose name starts with 'truth' is considered to be the truth set.	2010-01-28 21:41:23 +00:00
archive	Making a copy here before changing the live copy	2010-01-27 20:44:15 +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	added a wrapper exception for anything that goes wrong in VCF parsing; this way the problematic file line is emitted, no matter what happens. Makes debugging a lot easier, especially in large files.	2010-01-29 19:58:51 +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	Give the symlink on the webserver a name that would be a bit more obvious.	2010-01-28 00:40:20 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Quick script that changes "chr#" to "#" and "chrM" to "MT" and moves mitochondria to the end of the vcf; in accordance with the 1KG reference.	2010-01-28 21:59:33 +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	New Picard and SAM-JDK with automatic sequence name truncation	2010-01-11 20:49:13 +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	Fully qualify the target for the output file so that external build processes (aka firehose)	2010-01-26 23:06:30 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00