arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Feature request: allow stdin/stdout with maskfasta #155

Open bartgrantham opened 5 years ago

bartgrantham commented 5 years ago

I have a feature request: allow the maskfastacommand 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!