2 Commits (cc5d695bcf3574f0cadf4d5e5a1b395532c20bae)

Author	SHA1	Message	Date
depristo	ce51ffb56e	Oops, old local paths committed on accident. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5200 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-04 23:35:56 +00:00
depristo	29f3ad72f3	SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-04 22:27:05 +00:00