Ensure that vg rna produces unique HST names

[jeizenga]

Changelog Entry

To be copied to the draft changelog by merger:

• vg rna no longer projects transcripts twice onto a reference given by RS tag in a GFA
• vg rna assigns unique names to twice-projected transcripts on cyclic haplotypes

Description

There were a few overlapping bugs having to do with vg rna's projection algorithm when applied with new haplotype naming conventions. First, we were projecting reference transcripts back onto the reference whenever the reference was given as a W line with an RS tag. Second, when a transcript projected multiple times to the same haplotype (which can happen in cyclic, copy number variant genes) they were given the same identifier, which violated rpvg's assumptions downstream, leading to a crash.

[jeizenga]

Also, the development highlighted that some of the default VCF to GBWT behavior can be problematic for vg rna. Currently, haplotypes around unphased variants are extended into the region between variants from both sides. This leads to two haplotype blocks from the same haplotype covering the region, which can confuse vg rna into projecting onto the haplotype twice. This will only really be a problem in VCFs of quite low variant density, because the region between variants needs to cover a full transcript, so this probably won't show up in most use cases.