surject: realign anchors containing substitutions - #5010
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Changelog Entry
instead of accepting them through the exact-anchor shortcut.
Description
When one anchor chunk covered an entire surjection interval, surjection copied
the chunk directly and rescored it without realignment. This shortcut assumed
that the chunk represented an exact match.
Some mapper-produced chunks contain sequence-bearing substitution edits,
including ambiguous
Nbases. Applying the shortcut to these chunks couldproduce incorrect alignment scores, including large negative scores.
This change restricts the shortcut to chunks without substitutions. Chunks
containing substitutions follow the existing multipath realignment path.
It also initializes the interval sequence and base qualities before rescoring
a shortcut alignment.