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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Improve docs on --soft-filter argument. #2062

Closed SpikyClip closed 8 months ago

SpikyClip commented 8 months ago

I experienced some confusion trying to figure out why my filter tags were inversely being applied when using --soft-filter. I was under the initial impression that it applied STRING to records that meet the filter expression, just like how it applies STRING to any records that are in --mask-file.

In hindsight it makes sense that it is applied to things that fail to meet the expression, but I thought the documentation on --soft-filter could be improved to consider this discrepancy in behaviour between --mask-file and --include/--exclude. Especially considering it may not be immediately obvious as no errors are thrown.

pd3 commented 8 months ago

Thank you