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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Short option for write-index #2139

Closed mbhall88 closed 3 months ago

mbhall88 commented 3 months ago

I wonder if you would consider a short option for --write-index? I find myself using this option a lot and it would be nice for brevity's sake to have a shorter, single-char version.

pd3 commented 3 months ago

It is possible, -W would be a good choice and it is not taken.

jkbonfield commented 3 months ago

I grepped and found the only thing using -W was bcftools cnv, but that is totally undocumented in both usage and man page. It's something to do with the Baum Welch algorithm, but that's also undocumented in the man page. Is this an omission, or just an experimental feature that shouldn't be exposed to the users yet?

Anyway, cnv doesn't output VCF/BCF data so it doesn't need a --write-index option. Hence I agree that -W is a suitable short form. -W also isn't used much in samtools, so we could mirror the same logic over there if we desired.

pd3 commented 3 months ago

It is an experimental feature and I am happy for it to be disabled with a comment. Thank you

jkbonfield commented 3 months ago

No need to comment it out. I was just flagging it incase it was an error of documentation / usage.