Enable use of indices for large genomes

[jd3234]

This might be a general issue for medaka but I have only used medaka_variant so far.

Is your feature request related to a problem? Please describe. currently medaka only looks for bai etc indices. However, large genomes can't be stored in the default indices but only in csi

However, whatshap can also only handle small genomes as it expects vcf files indexed as tbi. They would also need to enable the use of vcf.gz.csi (I just ended up renaming the file and then restarted medaka to resume at the whatshap step again)

[cjw85]

Hi @jd3234,

As a piece of research software, I suspect this isn't something we will have time to implement. If you'd like to send a pull request making the changes necessary to output and use csi indexes I'm sure we can accomodate.