hanna 05aa928e3e Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1761 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-03 21:55:18 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x.	2009-10-03 21:55:18 +00:00
test/org/broadinstitute/sting	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).	2009-10-02 19:35:35 +00:00