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Looking good on a quick look through! Will have a proper look soon. |
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No rush - I'm just pushing here to be able to refer to it and for discussion when we're interested. |
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #830 +/- ##
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- Coverage 86.44% 0.00% -86.45%
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Files 18 6 -12
Lines 5651 2637 -3014
Branches 896 640 -256
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- Hits 4885 0 -4885
- Misses 593 2637 +2044
+ Partials 173 0 -173
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I'm bringing this branch up to date now with the intention of merging in as soon as it's usable. |
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from tree_sequence_builder and workign directly on the tree sequence instead. Initial dump of required HMM code First steps - isolated code works with shim Builder class Some more tests Remove TreeSequenceBuilder g Fake the sortedcontainers API for now Fully move to sorted lists of edges. Stuff Partial Abstract out the MatcherIndexes class Pull out stuff necessary for static match Compiling version without tree_sequence_builder Partway through getting C tests running add test dataq C code working and some tests Factor out the "output" struct in matcher Some basics for new Matcher infrastructure compiling with lwt interface partial update to use table collection Convert C code to use tables Roughly working Python-C infrastructure Add basic debug support to the MatcherIndexes Basic Python-C linkage works :hooray: Basic high-level infrastructure for matching Rename file Refactor the Matcher infrastructure Improve class infrastructure Add vestigial root automatically Fix up tests to remove hard-coded virtual root Work on making matcher work with edges not on site values Roughtly working version with edges on genome coords Python version looks like it's working Add sites_position storage and coordinate_t type Matching working in C (looks like) Infer start and end from haplotype Rough implementation of flank skipping Change python code to use coords in path Implement coordinate paths in C Implement some cludges to support initial zero site-paht Minor updates Sort-of working driver script Fiddle with some tricky issues Rename the test file to avoid collisions
16 tests across 4 hand-crafted tree topologies (star, binary, two-tree, deep chain) with exact path and mutation assertions from the current AncestorMatcher. These serve as regression tests when swapping to MatcherIndexes / AncestorMatcher2.
Update the AncestorMatcher2 Python wrapper so find_path accepts the same (h, start, end, match_out) arguments and returns the same (left, right, parent) tuple as the current AncestorMatcher. Remove Path, Match, find_match and zero_sites_path from matching.py. Move Path and Match to test_lshmm.py where they are used by the Python reference implementation.
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Just posting here for discussion, definitely not ready for merging any time soon.