Simpler lineage struct #2296
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Simpler lineage struct #2296
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #2296 +/- ##
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- Coverage 91.09% 90.96% -0.14%
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Files 20 20
Lines 11921 12003 +82
Branches 2435 2444 +9
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+ Hits 10860 10919 +59
- Misses 581 598 +17
- Partials 480 486 +6
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Cover all the easy cases Get SMCK working Add a "lineage" attr to Segment and fixup sweeps code Basic DTWF seems to work Fixup algorithms minimally
Make some progress. Disable DTWF tests for now Minimal changes to get smck working Fix DTWF simulations Fixup incorrectly failing test Make results reproducible by seed Revert back to old seed for failing test Skip segfaulting pedigree and sweep tests Fix sweeps Fix pedigree sims Keep track of lineages
Newer versions of jsonschema emit a DeprecationWarning
jeromekelleher
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I think this is the basic changes needed to start with. Would you mind having a quick look over to see if I've made any obvious mistakes (like keeping an msp_verify() left over from debugging etc) please @GertjanBisschop? |
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I'm going to go ahead and merge this, there's no point in keeping a big diff like this lying around. Sorry to anyone who's code is clobbered! |
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Work towards #2294
Work on adding a lineage struct that we store in the algorithm state in preference to using just segments. This does the initial bit where we just define this structure minimally in C and Python. Actually using it to some advantage can be done in follow-ups.