Use faidx file as genome file

[jma1991]

Version: bedtools v2.26.0-129-gc8b58bc

I'd like to use the faidx file produced by samtools as the genome file for bedtools. The first two columns of the faidx file are those in the genome file. Some of the bedtools commands accept the faidx file (shift, slop, flank, sort, random, shuffle, multiinter, bedtobam) without modification, and others require that the file is strictly two columns (intersect, closest, coverage, map, complement, subtract, jaccard). The error produced by these commands is the following:

Error: The genome file mm10.fasta.fai has no valid entries. Exiting.

It would be helpful if you could make this behaviour consistent. Personally I think it would be helpful to just allow usage of the faidx file with all commands. It saves having to create a separate genome file, or cutting those columns out of the faidx file in a pipe.

[arq5x]

I completely agree - there are two sets of "GenomeFile" code, and I will do my best to integrate them asap.

[arq5x]

This has been fixed and pushed to master.

[jma1991]

That's great, thank you very much 👍