asivache d72d332239 1) changed to search specifically for D and I cigar elements (and to process properly/ignore H,S,P elements) and print out only intervals that encompass actual indels. There's still one interval per read (at most) generated, which is the smallest intervals that covers ALL indels (D or I elements) present in the read; 2) if an interval (thus the original read itself and indels in it) sticks beyond the end of the chromosome, the read is ignored and this interval is NOT printed into the output; instead, a warning is printed to STDOUT (should we send it to logger.warn() instead? ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2385 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-16 23:29:07 +00:00
..
alignment	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00
analyzecovariates	Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.	2009-12-11 21:57:18 +00:00
gatk	1) changed to search specifically for D and I cigar elements (and to process properly/ignore H,S,P elements) and print out only intervals that encompass actual indels. There's still one interval per read (at most) generated, which is the smallest intervals that covers ALL indels (D or I elements) present in the read; 2) if an interval (thus the original read itself and indels in it) sticks beyond the end of the chromosome, the read is ignored and this interval is NOT printed into the output; instead, a warning is printed to STDOUT (should we send it to logger.warn() instead?	2009-12-16 23:29:07 +00:00
oneoffprojects	Added - new tests (Hapmap was re-added)	2009-12-14 21:57:20 +00:00
playground	Update documentation in the new help system	2009-12-16 21:33:12 +00:00
utils	Optimizations:	2009-12-16 21:39:58 +00:00