Feature request: New option --exclude for indexsplit

[andreas-wilm]

Hi Brent,

I would like to propose a new option for goleft indexsplit (and would have implemented it myself if my Go was any good): --exclude to be able to exclude chromosomes. A typical use case would be unplaced contigs, decoys etc. They are part of the BAM header, but usually you don't want to call variants on them. Sure, I can always remove them after running indexsplit, but then I cannot control the number of splits N properly.

Thanks, Andreas

PS: Thanks for Goleft!

[kpalin]

Second this and would implement is as bed file for exclusion regions.

Also reporting a documentation bug: --problematic parameter takes a bed file, not "pipe-delimited list of regions"