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@benjeffery benjeffery commented Oct 14, 2025

As mentioned at jeromekelleher/sc2ts#554

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codecov bot commented Oct 14, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.58%. Comparing base (4bf2521) to head (98c038d).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1059      +/-   ##
==========================================
+ Coverage   93.27%   95.58%   +2.30%     
==========================================
  Files          18       13       -5     
  Lines        6545     4753    -1792     
  Branches     1117      800     -317     
==========================================
- Hits         6105     4543    -1562     
+ Misses        299      159     -140     
+ Partials      141       51      -90     
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Can we just remove check for > num alleles instead?

ret = TSI_ERR_BAD_MUTATION_SITE;
goto out;
}
if (derived_state < 0 || derived_state >= (allele_t) self->sites.num_alleles[site]) {
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Is this what we did in the old branch, or did we just check for derived state being > 0? I can see checking for < 0 having value. I can't find the branch now either - is it on my fork

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In your branch (https://github.com/jeromekelleher/tsinfer/blob/experimental-hmm/lib/tree_sequence_builder.c#L420) you have:

    if (derived_state < 0) {
        ret = TSI_ERR_BAD_MUTATION_DERIVED_STATE;
        goto out;
    }

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Let's go with that then

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Great - changed over to just remove the allele count check.

@jeromekelleher jeromekelleher added this pull request to the merge queue Oct 15, 2025
Merged via the queue into tskit-dev:main with commit f25a008 Oct 15, 2025
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@benjeffery benjeffery deleted the remove-check branch October 15, 2025 11:16
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2 participants