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ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers
MIT License
128 stars 16 forks source link

With --details, add a SAM tag that shows the no. of identically scored best alignments #370

Closed marcelm closed 7 months ago

marcelm commented 7 months ago

This is the number of alignments among which we (pseudo-randomly) choose one to output.

Is this useful? I thought I needed this for debugging, but then never actually looked at the numbers.

Regarding the name of the tag: The old bwa aln used X0 for "Number of best hits", which I think is the same thing. There is a H0 tag in the SAM specification with the description "Number of perfect hits", which could be something similar, but I could not find what it is actually intended to be used for, so I went with X0.

This requires #368 to be merged first.

ksahlin commented 7 months ago

Could be nice for development. Perhaps it would be informative for downstream applications as well?

ksahlin commented 7 months ago

approved

marcelm commented 7 months ago

Perhaps it would be informative for downstream applications as well?

Yes, maybe? We could "promote" the tag to one that is output by default (even without --details), but I suggest we wait until users request it.