allow genetic_relatedness_vector to do windows that don't span the whole genome
#3003
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petrelharp
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #3003 +/- ##
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Coverage 89.80% 89.81%
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Files 29 29
Lines 31931 31979 +48
Branches 6179 6190 +11
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+ Hits 28675 28721 +46
- Misses 1860 1861 +1
- Partials 1396 1397 +1
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petrelharp
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petrelharp
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Sep 26, 2024
| @@ -9977,6 +9984,20 @@ tsk_matvec_calculator_init(tsk_matvec_calculator_t *self, const tsk_treeseq_t *t | |||
| tsk_memset(result, 0, num_windows * num_samples * num_weights * sizeof(*result)); | |||
| tsk_memset(self->parent, TSK_NULL, num_nodes * sizeof(*self->parent)); | |||
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| ret = tsk_tree_position_init(&self->tree_pos, ts, 0); | |||
| if (ret != 0) { | |||
| goto out; | |||
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this function always returns 0 currently
petrelharp
commented
Sep 26, 2024
| } | ||
| ret = tsk_tree_position_seek_forward(&self->tree_pos, index); | ||
| if (ret != 0) { | ||
| goto out; |
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I think this is ready to go - the only uncovered lines are not cover-able. |
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I've also put in the code here to let this work with arbitrary nodes. To see those changes separately look at the commits. |
petrelharp
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This looks good to go! (One test will need to be re-run but it failed for other reasons.) |
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jeromekelleher
approved these changes
Sep 27, 2024
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Pretty straightforward; and this allows parallelization across windows.
Edit: I've added into this the ability to pass in a different set of nodes (added here since it's on top of these changes).