Mauricio Carneiro 0e93cf5297 Taking care of bad cigars in the GATK ... * fixed BadCigarFilter to filter out reads starting/ending in deletion and that have adjacent I/D events. * added Unit tests for BadCigarFilter * updated all exceptions in LocusIteratorByState to tell the user that he can instead run with -rf BadCigar * added the BadCigar filter to ReduceReads and RealignTargetCreator (if your walker blows up with these malformed reads, you may want to add it too)		2012-03-20 14:32:57 -04:00
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net/sf	Fix serious engine bug that could cause reads to be dropped under certain circumstances	2012-02-13 16:25:21 -05:00
org/broadinstitute/sting	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00