Changes to get NM in output BAM.

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

MIT License

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Changes to get NM in output BAM. #271

Closed ernfrid closed 5 years ago

ernfrid commented 5 years ago

@brentp - The existing code doesn't report the number of mismatches from CRAM files.

This appears to be because they are calculated dynamically and tied to the decoding of the read sequence and the MD tag.

See https://github.com/samtools/htslib/blob/develop/cram/cram_decode.c#L1214-L1215 and https://github.com/samtools/htslib/blob/develop/cram/cram_decode.c#L1214-L1215

I'm somewhat guessing here, but only enabling MD5 decoding segfaults and adding in both seems to get the job done.

brentp commented 5 years ago

ouch. thanks for noticing that. cc @ryanlayer

ernfrid commented 5 years ago

Thanks Ryan!

ryanlayer commented 5 years ago

No, no. Thank you.

On Wed, Sep 26, 2018 at 8:56 PM Dave Larson notifications@github.com wrote:

Thanks Ryan!

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