Mauricio Carneiro 0d4027104f Reduced reads are now aware of their original alignments ... * Added annotations for reads that had been soft clipped prior to being reduced so that we can later recuperate their original alignments (start and end). * Tags keep the alignment shifts, not real alignment, for better compression * Tags are defined in the GATKSAMRecord * GATKSAMRecord has new functionality to retrieve original alignment start of all reads (trimmed or not) -- getOriginalAlignmentStart() and getOriginalAligmentEnd() * Updated ReduceReads MD5s accordingly		2012-01-26 17:06:36 -05:00
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net/sf	Revving Picard to incorporate final version of ReadWalker performance improvements.	2012-01-10 12:12:33 -05:00
org/broadinstitute/sting	Reduced reads are now aware of their original alignments	2012-01-26 17:06:36 -05:00