varlens-allele-support doesn't acceptable positional BAM argument

[iskandr]

I currently have to use the named parameter --reads since varlens-allele-support doesn't interpret its first argument as a BAM.

[timodonnell]

Agree it's confusing. varlens-reads takes bams as positional arguments and variants as --variants whereas varlens-variants takes VCFs positionally (and reads with --reads), i.e. the convention is the primary kind of input to each tool is positional and the others are named options. However, it's kind of a tossup whether variants or reads are the "primary" input the varlens-allele-support, since typically it would be called with both, so I went with just having them both be named arguments.

Given that logic, think it would be clearer if allele support took the reads as positional? It's true that the reads are always required whereas the variants are optional (you could specify --locus instead of giving a VCF)

[iskandr]

I would err on the side of consistency, even if it's a little awkward for one of the commands. Alternatively, I'd be happy with just always specifying --reads; the current mixed state is most confusing.