hanna 56bc4fa21a Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-04 18:20:20 +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	Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments.	2009-10-04 18:20:20 +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