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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gatk/walkers	Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads.	2013-05-29 16:41:01 -04:00
utils	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00