Smaller haplotype files

[jltsiren]

Changelog Entry

To be copied to the draft changelog by merger:

• Haplotype information files used in haplotype sampling are a bit smaller. Existing files can still be used.

Description

Haplotype information (.hapl) files used in haplotype sampling now use 32-bit integers when reasonable possible. This makes the files ~10% smaller. Old files can still be used.

GBWT construction from GAM/GAF precomputes some information used in GAF-base experiments and stores it in GBWT tags. This is experimental and can change at any moment.

Experimental vg haplotypes tools:

• Extract reference intervals and kmer counts for each subchain.
• Option to take all other non-duplicated candidate haplotypes as additional fragments in subchains that exceed a heuristic badness threshold.