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Missingness support in alignments #3317
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #3317 +/- ##
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Coverage 89.79% 89.80%
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Files 29 29
Lines 31056 31062 +6
Branches 5685 5687 +2
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+ Hits 27888 27894 +6
Misses 1779 1779
Partials 1389 1389
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This looks good - it's reassuring that there was so many tests that just needed to be enabled and seemed to work. Presumably I must have thought the details through when slogging through this the last time. |
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@jeromekelleher I've modified |
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Sgtm. Let's update the changleog and merge? Subsequent updates are just perf, right?
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Changlog added |
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LGTM. Spotted a typo
python/CHANGELOG.rst
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| **Breaking Changes** | ||
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| - The ``reference_sequence`` argument to ``TreeSequence.alignments`` is now required | ||
| to be the same length as the tree sequence. Previsouly it was required to be the length |
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| to be the same length as the tree sequence. Previsouly it was required to be the length | |
| to be the same length as the tree sequence. Previously it was required to be the length |
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STACKED ON #3313Fixes #1896
I've done this purely in Python so we can agree on the semantics and correctness before implementing in C.