ebanks a20ce1436d A temporary @hidden hack to get indel calling done for Phase I: don't try to call if there's too much coverage. Do not use this unless your last name rhymes with Shmoplin. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5348 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-01 19:22:27 +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	A temporary @hidden hack to get indel calling done for Phase I: don't try to call if there's too much coverage. Do not use this unless your last name rhymes with Shmoplin.	2011-03-01 19:22:27 +00:00
jna	After code review with APSG, trying a patch for SIGSEGV errors which checks the LSF result codes from lsb_openjobinfo instead of checking for a null return value from lsb_readjobinfo.	2011-02-08 21:08:22 +00:00
oneoffprojects	Generalized association is now working. Output is in a horrific format. Implementation of T-testing. Improvements are to look for classes dynamically (a la VariantEval/VariantAnnotator), beautify output, and do optimizations where they exist.	2011-03-01 01:23:37 +00:00
playground	Now makes all pairs, not only the good ones. The logic of selecting the "best" pair when the data are messy (e.g. multiple alignments available for an end) is still very naive	2011-02-24 16:21:26 +00:00
queue	Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.	2010-11-30 15:29:40 +00:00
utils	Generalized association is now working. Output is in a horrific format. Implementation of T-testing. Improvements are to look for classes dynamically (a la VariantEval/VariantAnnotator), beautify output, and do optimizations where they exist.	2011-03-01 01:23:37 +00:00