[cindykrafft]

Fixes #90.

calculatePalindromeDifferenceQuality divided two ints (-qual1 / 10), so a palindrome
mismatch cost int(Q/10): nothing below Q10, 1 for Q10–Q19, and so on. Simple mode
(calculateDifferenceQuality) and the README both use Q/10. This divides by 10.0f in the
two branches, as simple mode does.

Adds IlluminaPalindromeMismatchPenaltyTest: a 2x50 pair with a 42-base insert and two
Q19 errors scores 29.9 under the documented rule and must not be clipped at threshold 30
(it scores 31.7 with the integer penalty and was clipped); the same pair with one Q19
error scores 32.4 and must be clipped. The first test fails on unmodified main.

mvn -B test: 259 tests pass on main, 261 with this change.

Found in Mytochondria, a volunteer project that checks the numerical core of research software and verifies every finding by execution (methods and harnesses: https://github.com/cindykrafft/mytochondria/tree/main/audits/trimmomatic)

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[sebeier]

Thanks! Could you retarget this to the V0.42 branch so it makes it into the next release? And please drop the change to dependency-reduced-pom.xml, it seems to only change line endings from a local build.

[cindykrafft]

Thanks! Done: the branch is now a single commit on top of V0.42 with just the fix and the test, and the dependency-reduced-pom.xml change is gone (the shade plugin had rewritten it during my local build).

On V0.42, mvn -B clean verify passes with 519 tests (517 before), and the new test fails without the fix. Since the Build and Test workflow only runs for pull requests against main, there won't be a CI run on this PR now.

Happy to add a line to the 0.42 block of versionHistory.txt if you'd like one.

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