make_prg update PR series: 5. CLI changes

[leoisl]

1. Adds --suffix parameter to make_prg from_msa. This is in general useful, but it is actually required to use make_prg in a snakemake pipeline. The main issue I faced is that a snakemake pipeline is creating a dir of MSAs to be fed into make_prg from_msa, but currently just using the --input parameter and giving a dir as input tries to build a PRG from every file in the dir, including the .snakemake_timestamp file. This allows us to further filter out which files we want to build a PRG from;
2. Adds --long-deletion-threshold parameter to make_prg update. Current make_prg update implementation has issues dealing with long deletions, this parameter controls the size of the deletion we consider and ignore.

[mbhall88]

@leoisl just wondering if you have an ETA on this (and therefore v0.3)? I am working on drprg again which relies on make_prg, so it would be nice to use the latest conda version rather than the binary from your fork.

[leoisl]

I logged the last remaining comment as an issue and I am moving to submit more PRs so we can finally merge and release this