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18
issues of
abhinav
alts output is 0-based, yet junction output is 1-based. Might make sense to pick one of these for all output files.
When I use megadepth with `--alts`, the file output has a TSV extension though it's comma-separated. Can address the issue the obvious way, but I'm very happy to help change...
In many applications, it's useful to grep for variants by locus. It'd be very convenient if megadepth output wrote contig names instead of their corresponding numerical ids from the BAM,...