0e93cf5297
* 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) |
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