bgzipped and indexed reference fasta

[darked89]

Hello,

First things first: thank you so much for creating a very useful tool.

Modest enhancement proposal:

genomic fasta files are fairly big, so I tend to keep them compressed whenever possible.
Wold it be possible to modify perbase so it will be able to read bgzipped and indexed (samtools faidix) genome.fa.gz files as reference?

Darek Kedra

[sstadick]

I believe this should work by default. The reference and and its index are passed to the underlying htslib reader, which should support this.