Mark DePristo 41aba491c0 Critical bugfix for adapter clipping in HaplotypeCaller ... -- The previous code would adapter clip before reverting soft clips, so because we only clip the adapter when it's actually aligned (i.e., not in the soft clips) we were actually not removing bases in the adapter unless at least 1 bp of the adapter was aligned to the reference. Terrible. -- Removed the broken logic of determining whether a read adaptor is too long. -- Doesn't require isProperPairFlag to be set for a read to be adapter clipped -- Update integration tests for new adapter clipping code		2013-07-02 15:46:36 -04:00
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net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Critical bugfix for adapter clipping in HaplotypeCaller	2013-07-02 15:46:36 -04:00