retain more alignments#4923
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Changelog Entry
To be copied to the draft changelog by merger:
vg giraffechaining mode allows negative affine-gap alignment scores to be log-gap rescored before tossing out negatively scoring alignments (minor accuracy improvement)Description
I have confirmed that this improves read mapping for R10 reads at least (thousands of more reads aligned out of 1m) by rescuing many unmapped reads which can survive so long as their gaps get rescored. Correctness % stays about the same so these are good alignments we're rescuing.
Variant calling errors also tick down; for HiFi both indels and SNPs got better, and for R10 indels got better by more than SNPs got worse.