depristo 874406352c Accidentally commited the N2 comparing test as well... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5330 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-28 04:15:30 +00:00
..
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	Accidentally commited the N2 comparing test as well...	2011-02-28 04:15:30 +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	First general association module. Let the bug fixing begin!	2011-02-24 19:55:33 +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	Fixes for constrained movement Indel Realigner. Now sorts all of the reads in the interval before handing them to ConstrainedMateFixingSAMFileWriter to maintain correct contract between the two pieces of software	2011-02-28 03:52:18 +00:00