maf2bed

Used to convert multiple alignment format (MAF) files to a bed tabix-y style format. Used in jbrowse mafviewer plugin https://github.com/cmdcolin/jbrowse-plugin-mafviewer

Usage

Make sure to specify the 'assembly name' being used as the reference for the bed file as the first argument to maf2bed

zcat file.maf.gz | maf2bed assembly_name > file.bed
bgzip file.bed
tabix file.bed

Footnote

Converted to rust from perl as a coding exercise mostly, gaining a modest speedup on the way

Motivation

I wanted to try using the bigMaf (bigBed based) format ecosystem with large MAF files but bedToBigBed doesn't support streaming or reading compressed files(?), so that requires reading big files on disk and in memory. in contrast, MAF tabix type approach like implemented here can be compressed and streaming which allows much low memory usage and disk space