Add `.bai` as an optional output of samtools/merge

[maxulysse]

          ok, so could still have bai then

Can that be added in this PR?

Originally posted by @maxulysse in #4258 (comment)

[famosab]

Currently samtools only emits .crai not .bai. So this is still an issue!

[vagkaratzas]

Status on this one?