Add option to specify index location for idxstats.#2093
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jkbonfield
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| This option will allow the user to specify a customised index file | ||
| location. Example usage: samtools idxstat [options] -X </data_folder/data.bam> | ||
| [/index_folder/index.bai] |
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I'd be inclined to removed the <> and [] bits in this example for filename and index. See the EXAMPLES section of samtools-view.1 which has a -X option.
If not, then [...] is misleading as it implies it's optional, but when using -X it's mandatory.
Suggestion:
This option will allow the user to specify a customised index file
location. E.g.
.B samtools idxstats [options] -X /data/in.bam /index/in.bai
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I was following the example in samtools-depth.1.
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That's not using angle brackets though and it doesn't have the mandatory components in square brackets except where they're optional because the BAM filename was optional too). Ie it's essentially fn1 [fn2 ...] idx1 [idx2 ...].
Granted we're not great on consistency though.
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Add the -X option (used in some other tools) to specify the index location. Not entirely necessary because there is another way to do it, but this is a more straight forward way.
Fixes #2071.