Custom index pointer
Samtools [since a few months allows you to point to a custom index file](https://github.com/samtools/samtools/commit/c8c76865d81cebfa0eb9cf139155555fcf254a50) via the `-X` argument. Would you be able to implement a similar solution for scenarios where the index file doesn't live in the same directory as the BAM, has a different name, etc.?