hanna 5c6965575e Some refactoring that Mauricio and I worked through together. Changed filters ... to extend from org.broadinstitute.sting.gatk.filters.ReadFilter rather than directly from net.sf.picard.filter.SamRecordFilter, which allows us to add an initialize(GATKEngine) method so that filters can do any initialization they'd like based on CL arguments, SAM headers, etc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5760 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-04 19:29:08 +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	Removed -debug/--debug_mode.	2011-04-27 10:56:39 +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	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +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	Better header support when running R's read.table(...,header=T).	2011-05-03 19:56:20 +00:00
playground	- No longer prints out non confident calls (they were leading to tables that don't add up and confusing some Pacbio folk).	2011-05-04 19:26:55 +00:00
queue	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
utils	A walker to analyze the memory consumption of reference, reads, and RODs at	2011-05-03 17:08:15 +00:00