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Feature request: allow stdin/stdout with maskfasta
I have a feature request: allow the maskfasta
command to take -
as the filename for both -fi
and -fo
to allow piping fasta files through maskfasta. So something like this would be possible
zcat unmasked.fa.gz | bedtools maskfasta -bed mask.bed -fi - -fo - | gzip -c - > masked.fa.gz
Even better if it did this by default:
zcat unmasked.fa.gz | bedtools maskfasta -bed mask.bed | gzip -c - > masked.fa.gz
Thank you for the consideration!