CIGAR string option to use "M" instead of "=" or "X" for compatibility

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

Apache License 2.0

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Closed rnpandya closed 12 years ago

bolosky commented 12 years ago

I added a -M option, which will cause the CIGAR string generator to use M rather than = and X.