surject: classify disjoint interval alignments

[Sagorikanag]

Changelog Entry

To be copied to the draft changelog by merger:

• vg surject -u related changes

Description

• discover separated surjection intervals independently of supplementary option
• classify non-best alignments with more than 4 bp of query overlap as secondary
• emit supplementary alignments only when requested

Motivation

Interval discovery was conditional on supplementary reporting, coupling alignment
candidate generation to output selection. This separates those decisions and
classifies the resulting alignments according to their query overlap. Before, alignments
to distant but similar regions on the same path, such as segmental duplications
merged unless -u was used. When separated, every non-best alignment was labeled
supplementary, even if it covered the same part of the read and was really an alternative
mapping. Now, distant regions are always evaluated separately. A non-best alignment
overlapping the best by more than 4 bp of the read is secondary; a mostly disjoint alignment
is supplementary and emitted only with -u.