Mauricio Carneiro f73ad1c2e2 Bugfix/Rewrite: Algorithm to determine adaptor boundaries ... The algorithm wasn't accounting for the case where the read is the reverse strand and the insert size is negative. * Fixed and rewrote for more clarity (with Ryan, Mark and Eric). * Restructured the code to handle GATKSAMRecords only * Cleaned up the other structures and functions around it to minimize clutter and potential for error. * Added unit tests for all 4 cases of adaptor boundaries.		2011-12-20 17:48:39 -05:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Bugfix/Rewrite: Algorithm to determine adaptor boundaries	2011-12-20 17:48:39 -05:00