carneiro 3de300e504 A walker that moves annotations from the filter field to the info field of truth annotated vcfs. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5458 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-17 17:11:28 +00:00
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alignment	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
analyzecovariates	Change to support plotting of indel quality as a function of covariates - for now, just call different R calling script.	2011-01-22 14:09:23 +00:00
commandline	<key>=<value> tagging support for command-line arguments. Unfortunately, still	2011-01-21 00:22:42 +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	Probable patch to Jerry Glenn's GetSatisfaction report. I'm having him test it out.	2011-03-17 16:00:50 +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	A walker that moves annotations from the filter field to the info field of truth annotated vcfs.	2011-03-17 17:11:28 +00:00
playground	An extremely basic implementation of a deBruijn-based local assembler, using the jgrapht graph library. This is not at all optimized and has only been tested on my very simple 3-read test bams. I'm sure there are bugs in there - more testing coming soon. Insertions and deletions confirmed to generate identical graphs (except for the multiplicity of edges of course). Not worth using yet.	2011-03-17 14:03:07 +00:00
queue	Added a new @PartitionBy for walkers to specify how to cut up their inputs.	2011-03-12 01:33:08 +00:00
utils	GenotypeAndValidate: now looks at annotations in the INFO field instead of filter field. Better output and filters repetitive calls to indel extended events.	2011-03-15 21:54:40 +00:00