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add keep_unary for pedigrees and dtwf #2145
add keep_unary for pedigrees and dtwf #2145
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Nice! @sgravel I think this should more-or-less do what we want with the pedigree sims, so we could start thinking about trying it out and seeing what we get? |
Perfect! Presumably this does not record the ancestors above the MRCA yet, right? |
Yes, that's correct @sgravel. This would require an additional flag indicating the stopping point of the simulation. We have been discussing this exact issue though while thinking about potential performance improvements (see #2121). |
Ok, we'll do some testing! |
Let's update this and get it merged I think @GertjanBisschop - I guess we should try to register some issues for any remaining TODOs and corner cases so we don't forget them. We can update to the new API later. |
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Codecov Report
@@ Coverage Diff @@
## main #2145 +/- ##
==========================================
- Coverage 91.45% 91.38% -0.08%
==========================================
Files 20 20
Lines 11170 11199 +29
Branches 2268 2280 +12
==========================================
+ Hits 10216 10234 +18
- Misses 521 529 +8
- Partials 433 436 +3
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Continue to review full report at Codecov.
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Not sure how I might have reduced code coverage that significantly. What do I do to fix this? |
Right I guess this means I'll have to write some additional tests in C. |
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Let's have a look through this tomorrow @GertjanBisschop - it might be simpler to push through the final API rather than getting the C test coverage up. |
Implemented in #2176. |
This pull request stores all nodes through which some ancestral material passes for pedigrees and dtwf simulations when the flag
record_unary=True
is set. This is a first pass to allow for testing (see #2132).This pull request requires defining a
MSP_NODE_IS_PASS_THROUGH_EVENT
(see ). Is this as simple as simply using the next available number in line (#define MSP_NODE_IS_PT_EVENT (1u << 22)
)?As with #2130 unit tests are still basic and require further work.