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
..
config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Reduced reads are now aware of their original alignments	2012-01-26 17:06:36 -05:00
test	HaplotypeCaller now uses insertions and softclipped bases as possible triggers. LocusIteratorByState tags pileup elements with the required info to make this calculation efficient. The days of the extended event pileup are coming to a close.	2012-01-26 15:56:33 -05:00