-= doesn't work in SAM - Githubissues

amplab / snap

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

https://www.microsoft.com/en-us/research/project/snap/

Apache License 2.0

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-= doesn't work in SAM #148

Closed bolosky closed 2 years ago

bolosky commented 2 years ago

The alternate form of CIGAR strings that you get by using -= (where identical bases have an = CIGAR code and SNVs have an X rather than both being included in M) causes CIGAR string validation to fail when writing SAM output (but not BAM).

bolosky commented 2 years ago

Fixed in 2.0.1