Mark DePristo d20be41fee Bugfix for FragmentUtils.mergeOverlappingPairedFragments ... -- The previous version was unclipping soft clipped bases, and these were sometimes adaptor sequences. If the two reads successfully merged, we'd lose all of the information necessary to remove the adaptor, producing a very high quality read that matched reference. Updated the code to first clip the adapter sequences from the incoming fragments -- Update MD5s		2013-04-25 11:11:15 -04:00
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java	Bugfix for FragmentUtils.mergeOverlappingPairedFragments	2013-04-25 11:11:15 -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