Question: does pbmm2 modify MM and ML tags for supplementary alignments with hard clippings?

[lh3]

@armintoepfer, here is a pbmm2 question for you. PacBio now outputs MM/ML tags for methylation. When pbmm2 outputs a supplementary alignment with hard clippings, does it modify the original MM/ML, copy them over to the output SAM line, or discard MM/ML on hard clipped SAM line? For the context, see samtools/hts-specs#646, but you don't have to read the thread.

[armintoepfer]

Hey @lh3, pbmm2 never hard clips. All of our alignments are either primary or supplementary with soft clippings.

[lh3]

Got it. Thanks!