aaron ba67c7f02b added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-02 21:09:18 +00:00
..
alignment	Fixed collection of bugs in reads aligning to multiple locations.	2009-11-02 04:02:09 +00:00
gatk	added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals	2009-11-02 21:09:18 +00:00
playground	-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).	2009-11-01 05:35:47 +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	New PackageUtils interferes with the packaging utility. Revert until Aaron and	2009-11-02 19:14:14 +00:00