Do radius doubling on final round of optimization #223
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Add option to include nt mutations in taxonium export
Add option to output closest relative(s) per sample
New matUtils Features
…sher-matoptimize-fuse
…matoptimize-fuse
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MatOptimize will always reassign the states again to minimize back mutations. |
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This is also going to fix #219. Both usher and matoptimize in this pull request use a numeric ID to identify nodes. Node name is an optional attribute stored separately in a hash table. |
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The labels are in the format of "Parsimony score increase threshold for running interim optimizations"_"Maximal time (in minutes) to run interim optimizations". Inf means no interim optimization is run. 2 hours (radius doubled from 4 to 16) of optimization is run in the end.
There is no significant impact of interim optimizations on parsimony score (difference ~0.0012% between max and min), perhaps because the sample placed are close in time. Maybe I should disable interim optimization by default for daily tree maintenance?
This is the result of placing 47853 samples onto a tree with 8468197 samples on 2*10 threads of Xeon(R) Silver 4216 CPU @ 2.10GHz.