Ls missingness #2515
Ls missingness #2515
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Codecov Report
@@ Coverage Diff @@
## main #2515 +/- ##
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Coverage 89.83% 89.83%
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Files 30 30
Lines 28624 28624
Branches 5590 5590
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Hits 25713 25713
Misses 1655 1655
Partials 1256 1256
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astheeggeggs
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| @@ -246,6 +250,8 @@ def stupid_compress_dict(self): | |||
| u = tree.parent(u) | |||
| self.N[self.T_index[u]] += 1 | |||
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| print(self.T) | |||
| else: | ||
| query_is_hom = np.logical_not(query_is_het) | ||
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| EQUAL_BOTH_HOM = np.logical_and( |
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All caps like this is usually reserved for constants (https://peps.python.org/pep-0008/#constants) is there a convention here that I'm not seeing?
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Let's update this and merge |
astheeggeggs
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Can you squash the commits again please @astheeggeggs? Something has gone a bit haywire, there should only be one commit by the end. (I'm happy to do it, if you prefer) |
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Yeah, would you mind? I've merged the various conflicts and have checked all the tests I wrote are passing. Seems fine, but my rebasing skills are terrible. |
Added forwards backwards testing and now include missingness appropriately added missingness to diploid LS added some fixes for flake errors added missingness to diploid viterbi changed test_genotype_matching_fb.py remove stray print removed caps for bool EQUAL_BOTH_HOM etc Removed caps for EQUAL_BOTH_HOM etc in Viterbi removed unused imported function
jeromekelleher
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done - should merge automatically now |
Missingness added to forwards-backwards diploid LiS testing
Added missingness, by including an emission probability of 1 for all missing characters in the query sequence.