Mwu biasz int64 - #2598
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Mwu biasz int64#2598
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calc_mwu_biasZ() summed the tie adjustment (p*p-1)*p, the pair counts and the group sizes in `int`. The tie term is cubic in the number of reads sharing one quality or position bin and exceeds INT_MAX once a bin holds 1291 reads. That happens at a single deep site (-d raised for amplicon, mitochondrial or viral data) and, under the default -d 250, across the samples of a multi-sample call: the histograms are pooled over all samples, so ~45 samples at 30x with MAPQ 60 are enough. The wrapped tie term inflated the variance and shrank INFO/MQBZ, BQBZ, RPBZ, SCBZ, MQSBZ and NMBZ towards zero (for example MQBZ -7.9 where the tie-corrected Z is -36.6 for 1300 MAPQ-60 reference reads and 40 MAPQ-30 alternate reads). Accumulate in int64_t. Adds a regression test with 1340 20-bp reads where the MAPQ-60 bin holds 1300 reads, and a NEWS entry. Assisted-by: Claude:claude-fable-5-1 Signed-off-by: Cindy Krafft <cynthiacondra@gmail.com>
The previous commit avoids overflow by switching to 64-bit, but it moves overflow from ~2^10 to ~2^21. While high (approx 2 million depth) this commit refactors it to remove the cube entirely. Also shrunk the test data a little by using a higher compression level. Assisted-by: Claude:claude-opus-5-5 high Signed-off-by: James Bonfield <jkb@sanger.ac.uk>
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A replacement for #2595. Fixes #2594
This has the same commit as 2595 but with an additional refactoring. The two commits are left in place to reflect the same authorship (although by author we mostly mean Claude!), but also because the earlier commit is perhaps easier to understand as an interim solution top the original problem.