Faster GBWT construction from GAM/GAF

[jltsiren]

Changelog Entry

To be copied to the draft changelog by merger:

• GBWT construction from a GAM/GAF file now uses parallel construction jobs.

Description

If instructed to use m construction jobs, the new algorithm will partition the graph into approximately m jobs, but often a bit more. A separate GBWTBuilder will be created for each job. The algorithm reads the GAM/GAF file using m threads, and each read is sent to the appropriate builder. This obviously works better with shuffled reads than sorted reads.

Some additional changes:

• I got rid of the old path/thread terminology in vg gbwt and in some other places.
• GBWT construction options have been removed from vg index. They had likely diverged from the supported ones in vg gbwt anyway.
• SDSL, GCSA2, GBWT, and GBWTGraph have been updated.

[adamnovak]

It looks like we need to make a corresponding change in toil-vg for the removal of vg index --gbwt-name, or else rip toil-vg out of CI and do something else for testing the pipelines.