This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
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.
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 appliedSTRING
to records that meet the filter expression, just like how it appliesSTRING
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.