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make the meaning of -s options in samtools depth subcmd more clear#1355

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wulj2 wants to merge 1 commit intosamtools:developfrom
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make the meaning of -s options in samtools depth subcmd more clear#1355
wulj2 wants to merge 1 commit intosamtools:developfrom
wulj2:develop

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@wulj2
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@wulj2 wulj2 commented Jan 6, 2021

in fact, the -s option will automatically raise baseQ threshold to 1 internally.
see https://github.com/samtools/samtools/blob/develop/bam2depth.c#L172-L175
so the document of -s option is somewhat misleading?

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valeriuo commented Jan 7, 2021

Merged as fe8efa7
Thanks for the fix!

@valeriuo valeriuo closed this Jan 7, 2021
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