@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, 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.