James Bonfield

Oops yes :). Anyway, we discussed it as a team and thought your proposal to be the right approach, so thanks.

Well the PR now exists, so it's a moot point. :-) However I do obviously understand that long read technologies exist. I also understand that they can, in some specific...

I'll need to think about it more, but in answer to the final question, implementing a PL: tag on `@PG` is easy to do and I think some form of...

If you only have a single stage of scatter gather, the per read `@PG` could refer to one of the scatter stages rather than the terminating post-gather PG record. I...

Apologies for forgetting about this one. The pseudocode does indeed play a bit fast and loose at times with regards to parameters and return values. It's intended to be understandable...

The consequence of adding more fields to sum over into the consensus algorithm is a small performance drop, but it's not tragic. On 10MB region of PacBio CCS GIAB HG002...

Strictrly for local users wishing to evaluate, my command is: ``` cd ~jkb/lustre/GIAB/chr1 samtools consensus -X pacbio-ccs -@8 -C0 -A -r chr1:10M-20M --show-ins yes --show-del no -f pileup HG002.GRCh38.PacBio_CCS_15Kb.bam |...

I found that I can use `--mark-ins lc --mark-del "*"` and `tr -d '[a-z]'` to remove the insertions and add back the deletions. That works, but maybe this could be...

A related issue to this is for ambiguity codes. The IUPAC codes have always been incomplete. We can use `R` to mean `A` or `G`, but there is no ambiguity...

I'm happy with the new text, although I note it's draft still. PS. The rendering of the diff PDF is visible in Opera and MS Edge on Windows, but firefox...