Fix bcftools stubs to behave like program

[fellen31]

This PR fixes issues where the stubs doesn't behave like the program would.

I.e. running bcftools with --output-type u/b --write-index=tbi, it still outputs a csi index, but were outputting a tbi index in the stubs:

• --output-type v --write-index=tbi - error
• --output-type v --write-index=csi - error
• --output-type z --write-index=tbi - tbi index
• --output-type z --write-index=csi - csi index
• --output-type u --write-index=tbi - csi index <- note
• --output-type u --write-index=csi - csi index
• --output-type b --write-index=tbi - csi index <- note
• --output-type b --write-index=csi - csi index

It takes the custom function added for bcftools csq in #6605, together with a similar function for the index, and applies it to the applicable modules.

PR checklist

Closes #XXX

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