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Short option for write-index #2139

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mbhall88 opened this issue Mar 26, 2024 · 4 comments
Closed

Short option for write-index #2139

mbhall88 opened this issue Mar 26, 2024 · 4 comments

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@mbhall88
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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
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pd3 commented Mar 26, 2024

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

@pd3 pd3 mentioned this issue Mar 26, 2024
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@jkbonfield
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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.

jkbonfield added a commit to jkbonfield/bcftools that referenced this issue Mar 26, 2024
@jkbonfield
Add short option -W for --write-index.
003a723 
Given --write-index now takes an optional argument, and optional long
options are --long-opt=arg and short options are -larg, I chose to
also accept -l=arg for the sake of consistency and ease of
documentation.  The standard -larg still works too.

If we wish to stick strictly to the normal conventions, then this is a
trivial change in version.c (and a search and replace in the
documentation).

Also fix formatting bug in bcftools merge man page section leading to
a lot of underlined text.

Fixes samtools#2139
@pd3
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pd3 commented Mar 27, 2024

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

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

@pd3 pd3 closed this as completed in ca95dfe Mar 28, 2024
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3 participants
@pd3 @jkbonfield @mbhall88