# 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

## Install

```
cargo install maf2bed
maf2bed --help
```

## Usage

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

```
#non parallel compression/decompression
zcat file.maf.gz | maf2bed assembly_name | bgzip > file.bed.gz
#parallel compression/decompression
pigz -dc file.maf.gz | maf2bed assembly_name | bgzip -@8 > file.bed.gz

tabix file.bed.gz
```

Might also need a sort -k1,1 -k2,2n in some cases on the bed file before
bgzip/tabix

## Footnote

Converted to rust from perl as a coding exercise mostly, gaining a modest
speedup on the way https://twitter.com/cmdcolin/status/1719608993310486883

## 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 lower memory usage and disk space