Eric Banks d976aae2b1 Another fix for the Indel Realigner that arises because of secondary alignments. ... This time we don't accidentally drop reads (phew), but this bug does cause us not to update the alignment start of the mate. Fixed and added unit test to cover it.		2013-06-21 16:59:22 -04:00
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java	Another fix for the Indel Realigner that arises because of secondary alignments.	2013-06-21 16:59:22 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00