Eric Banks a5a68c09fa Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads. ... The problem ultimately was that ReadUtils.readStartsWithInsertion() ignores leading hard/softclips, but ReduceReads does not. So I refactored that method to include a boolean argument as to whether or not clips should be ignored. Also rebased so that return type is no longer a Pair. Added unit test to cover this situation.		2013-05-29 16:41:01 -04:00
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java	Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads.	2013-05-29 16:41:01 -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