Remove use of C variables starting in _ from bam_consensus.c.#2250
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jmarshall
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Aug 12, 2025
This conflicts with _P definition in newlib's ctype.h in cygwin. Fixes samtools#2248
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The defaule Bayesian method does a lot of local modification of mapping quality via the local mismatch count. This is floating point based, but the variable being integer means lots of unnecessary type conversions happen. It's surprising this is such a significant performance cost compared to everything else that goes on (including a division which can be avoided using lookup tables, but isn't significant).
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I also added another tiny commit which isn't technically related to the original issue, but I don't feel like creating multiple PRs and then someone having to deal with resolving any conflicts plus having to do all the testing and evaluation twice. For local users, my assessment was on this file: The md5sum consensus didn't differ, but the |
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This conflicts with _P definition in newlib's ctype.h in cygwin.
Fixes #2248