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Implement NONCOPY for the diploid case #64

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merged 1 commit into from
Jun 1, 2024

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@szhan szhan commented Jun 1, 2024

Fix #58

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szhan commented Jun 1, 2024

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.

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szhan commented Jun 1, 2024

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

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szhan commented Jun 1, 2024

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

@szhan szhan force-pushed the noncopy branch 2 times, most recently from ca0a0f3 to 391d3c4 Compare June 1, 2024 18:06
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szhan commented Jun 1, 2024

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.

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szhan commented Jun 1, 2024

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.

@astheeggeggs astheeggeggs merged commit 8f5cf2d into astheeggeggs:main Jun 1, 2024
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Implement NONCOPY for the diploid case
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