Update the fingerprinting script in the workflow to accept/ignore the AH records in @sq lines. No need to update statistics or so. Lost reads (instead aligning to ALT contigs) should just be ignored.
- Either update pysam (probably overkill for a small script like bsnp.py)
- ... or manually remove the AH records from the @sq lines before parsing them.
Update the fingerprinting script in the workflow to accept/ignore the AH records in @sq lines. No need to update statistics or so. Lost reads (instead aligning to ALT contigs) should just be ignored.