Filter out reads with wonky cigar strings.
- No reads with Hard/Soft clips in the middle of the cigar
- No reads starting with deletions (with or without preceding clips)
- No reads ending in deletions (with or without follow-up clips)
- No reads that are fully hard or soft clipped
- No reads that have consecutive indels in the cigar (II, DD, ID or DI)
ps: apparently an empty cigar is okay...
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GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51.