Is your feature request related to a problem? Please specify.

Right now, after extracting sequences with samtools faidx, one has to afterwards generate the FAI and GZI files.

Describe the solution you would like.

It would be nice if it was possible to automatically generate these files from the fasta output from samtools faidx (similar to samtools view --write-index):

samtools faidx -r targets.regions --write-index --output targets.fas.gz sequences.fas.gz