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Drop haplotype matcher code - #3499
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jeromekelleher merged 1 commit intoOct 30, 2026
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #3499 +/- ##
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+ Coverage 91.68% 91.71% +0.03%
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Files 38 37 -1
Lines 32242 30831 -1411
Branches 5155 4919 -236
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- Hits 29560 28278 -1282
+ Misses 2346 2223 -123
+ Partials 336 330 -6
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The Li and Stephens HMM (tsk_ls_hmm_t and the compressed and Viterbi matrices) is replaced by the tsls package, which tsinfer and sc2ts use. Nothing else in the library uses it. Remove the low-level haplotype matching classes _tskit.LsHmm, CompressedMatrix and ViterbiMatrix wrapped the C haplotype matching code removed in the previous commit, and were never public API. Their tests compared against the lshmm package, which is no longer needed. The tests that were worth keeping are ported to tsls.
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This is a straightforward improvement, that's been long-planned, so merging. |
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This is superceded by https://github.com/tskit-dev/tsls/, which absorbs all functionality and is many times faster.
As the API is private, the only real impact on users is that C builds will need to change, if they are building in haplotype_matching.c