Diploid map interleaved

[Sagorikanag]

Changelog Entry

• vg surject --diploid-map --interleaved now evaluates alternative paired graph placements jointly using haplotype alignment scores and the learned fragment-length distribution.

Description

This PR adds paired short-read support for vg surject --diploid-map --interleaved.

Consecutive alternative placements for the same fragment are grouped and surjected to both sample haplotypes. Compatible mate combinations are enumerated and scored using their combined alignment score and, once available, the learned fragment-length distribution.

The highest-scoring candidate pair becomes the overall primary pair. Alternative compatible placements are emitted as secondary pairs, while supplementary or otherwise unpaired surjections are emitted separately with appropriate mate information.

Fragment-length learning initially runs serially using high-confidence pairs. Ambiguous fragments are buffered until the distribution is available, after which processing continues in parallel.

The output uses:

• hp for the preferred or alternative haplotype placement;
• hq for confidence in the haplotype selection;
• aq for the original graph-alignment mapping quality;
• MAPQ (GlobalQ) for confidence in the globally selected paired placement.

This PR depends on:

• the long-read --diploid-map vg changes;
• Add grouped parallel I/O for graph placements of interleaved reads libvgio#95.

This is currently a stacked draft PR and will be rebased onto master after its dependencies merge.