rpoplin 06ff81efe5 Added NeighborhoodQualityWalker.java and ReadQualityScoreWalker.java which are used to calculate a read quality score based on attributes of the read and the reads in the neighborhood. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1922 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-28 13:24:11 +00:00
..
alignment	Read uints directly into longs.	2009-10-15 16:15:11 +00:00
gatk	Trivial protection for null value	2009-10-27 21:52:52 +00:00
playground	Added NeighborhoodQualityWalker.java and ReadQualityScoreWalker.java which are used to calculate a read quality score based on attributes of the read and the reads in the neighborhood.	2009-10-28 13:24:11 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	code cleanup and containsStartPosition function	2009-10-27 21:53:40 +00:00