--force_phasing True on toil-vg construct doesn't work

[adamnovak]

I ran toil-vg construct with --force_phasing True and vg 1.20.0 when building a GBWT from a VCF set that has phase breaks (1000 Genomes on GRCh37).

The resulting GBWT did not have all contig-length haplotypes in it; there were still phase breaks.

We need to add a test for this option at a small scale, and then work out why it doesn't work (at least with construct) and fix it.

[adamnovak]

Jouni says the real problem may be that we don't have a way to pass --discard-overlaps, which also causes phase breaks.

[adamnovak]

We also need a way to cover contigs with no VCFs with at least one GBWT thread for the primary path. I'm not sure if we do that already.