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Added methods to sort and squash segments in the IbdFinder output. #2460
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Codecov Report
@@ Coverage Diff @@
## main #2460 +/- ##
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Coverage 93.43% 93.43%
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Files 28 28
Lines 27401 27401
Branches 1255 1255
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Hits 25601 25601
Misses 1766 1766
Partials 34 34
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Made some small changes to ibd.py to ensure consistent behaviour in tests
Hey @hyanwong! Unfortunately, we both made some pretty involved changes to the test_highlevel.py file in the past few days. I think I've fixed up the merge conflict, but I can't figure out how to get my tests to run with the argument that I added into |
It was @benjeffery who fixed up |
I'll take a look now |
I think the simplest thing here is to remove |
Thanks @benjeffery and sorry for the late reply -- I had to take a few days off to deal with some urgent moving-to-the-US things.
I added this argument because some of my changes in this PR make IbdFinder run much more slowly, to the point where they look like they're hanging. (This is likely a Python-specific problem -- as we discuss in #2459, the C code works differently because it uses an AVL tree to do the sorting). But I didn't want to omit the tests entirely, as they cover some useful edge cases, so I wanted to run them with smaller sample sizes than the ones hard-coded in. |
We can leave the slow examples in the examples - but skip them in these tests? |
Fixes #2459 -- see the issue for discussion about why this is needed. Draft only at the moment.
PR Checklist: