avoid underflow

[faithokamoto]

Changelog Entry

To be copied to the draft changelog by merger:

• Avoid underflowing multiplicities in vg giraffe chaining mode (caused erroneous MAPQ 0)

Description

We had been managing to underflow chain_count_by_alignment here such that multiplicities got set as just around the maximum value for a size_t. Such high multiplicity guaranteed a MAPQ of 0.

This will not change the alignments output. It will likely "rescue" some MAPQ 0s, including some that represent incorrect alignments, and that will change variant calling. I have not tested the extent of the change.

[faithokamoto]

In my tests, this changes between 0.2% to 0.8% of mapping qualities, most of which used to be 0. In R10 reads some of those are rescued all the way to 60. HiFi reads tend to get rescued to single-digit MQs. Unfortunately it rescues more wrong MQ0s than correct MQ0s... I'll run variant calling tests next.