depristo 541c9109b3 V1 of GATK Resource Bundling system ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5659 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-18 19:23:45 +00:00
..
alignment	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
analyzecovariates	It was returning 1 when it should return 0	2011-03-31 20:50:38 +00:00
commandline	Catch samtools exceptions and make them 'BAM Exceptions' asking the user to run Picard's validator and re-index the file before posting anything to the forum. Let's see whether this helps or not.	2011-04-18 03:52:43 +00:00
datasources/pipeline	FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait.	2011-02-17 19:09:03 +00:00
gatk	V1 of GATK Resource Bundling system	2011-04-18 19:23:45 +00:00
jna	Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays.	2011-03-10 22:58:54 +00:00
oneoffprojects	Spurious associations can develop from including ambiguous reads in these tests. Perhaps MQ0 reads shouldn't be used for anything except MQ0, but the best way to do that is to restructure the code, so for now I'll put it off.	2011-04-17 23:17:03 +00:00
playground	Throwing an error if INFO fields arguments contain whitespace.	2011-04-15 20:52:55 +00:00
queue	Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean].	2011-04-08 18:44:32 +00:00
utils	Centralizing a bunch of Broad specific utility functions from code scattered in GSA-Firehose, PipelineTest, custom QScripts, etc.	2011-04-13 21:29:02 +00:00