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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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Incorrect CIGAR string found #140

Closed m-bogaerts closed 2 years ago

m-bogaerts commented 2 years ago

I had an issue with the CIGAR string, since it is expecting to find I/D/H/S/X/= but I have also D and M in my CIGAR. Is there any procedure to "clean" the CIGAR?

Thank you in advance.

Reading BAM/SAM file - ERROR - syri:130 - Incorrect CIGAR string found. CIGAR string can only have I/D/H/S/X/=. CIGAR STRING: 231M5D199M6I199M3D112M1I140M138D256M7D703M2I313M497838H

mnshgl0110 commented 2 years ago

The aligner should have an option to output CIGAR with X/= instead of M. In minimap2, this can be done using the --eqx parameter.