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astheeggeggs / lshmm

code to run Li and Stephens
MIT License
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Implement NONCOPY for the diploid case #64

Closed szhan closed 1 month ago

szhan commented 1 month ago

Fix #58

szhan commented 1 month ago

The tests test_ts_simple_n8_high_recomb in TestNonTreeViterbiDiploid seem stuck. The CI runs started two hours ago, and they still haven't finished.

szhan commented 1 month ago

The naive implementations of the diploid Viterbi algorithm are taking too long when the ref. panel size gets too large when including ancestral haplotypes.

szhan commented 1 month ago

A workaround is to only run the naive implementations of diploid Viterbi when not including ancestors in the ref. panels.

szhan commented 1 month ago

Alternatively, we could check the size of the ref. panel when including ancestors. If it exceeds a certain threshold, say n = 100, then don't run the naive implementations of diploid Viterbi.

szhan commented 1 month ago

For now, when the ref. panel size exceeds 100, the naive implementations of diploid Viterbi are not run. There is probably a better way to do this.