rpoplin 0b1e243a7b CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-10 15:52:20 +00:00
..
annotator	- Fixed output for beagle header	2010-01-21 21:25:56 +00:00
concordance	Check for division by 0 in annotations	2010-01-07 19:27:15 +00:00
fasta	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
filters	VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful	2010-01-29 12:13:08 +00:00
genotyper	Various improvements and fixes:	2010-02-07 04:21:04 +00:00
indels	RealignerTargetCreator is officially live	2010-01-27 03:41:52 +00:00
recalibration	CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard	2010-02-10 15:52:20 +00:00
varianteval	Reverting	2010-02-05 15:57:09 +00:00
DepthOfCoverageIntegrationTest.java	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
PileupWalkerIntegrationTest.java	Now that we changed how deletions are represented, got to update MD5...	2009-12-30 22:00:58 +00:00
PrintReadsWalkerTest.java	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).	2009-10-02 19:35:35 +00:00