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Will-Tylerjeromekelleher
Will-Tyler
authored and
jeromekelleher
committed
Update unit tests
1 parent 65c6963 commit d52069b

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-115
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2 files changed

+21
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lines changed

‎bio2zarr/vcf2zarr/icf.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -598,6 +598,7 @@ def compute_lpl_field(variant, laa_val: np.ndarray) -> np.ndarray:
598598
pl_val = np.broadcast_to(pl_val, n.shape)
599599
row_index = np.arange(pl_val.shape[0]).reshape(-1, 1)
600600
lpl_val = pl_val[row_index, n]
601+
lpl_val[b == constants.INT_FILL] = constants.INT_FILL
601602

602603
return lpl_val
603604

‎tests/test_vcf_examples.py‎

Lines changed: 20 additions & 115 deletions
Original file line numberDiff line numberDiff line change
@@ -446,41 +446,41 @@ def ds(self, tmp_path_factory):
446446

447447
def test_call_LAA(self, ds):
448448
call_LAA = [
449-
[[1, -2, -2], [1, -2, -2]],
450-
[[1, -2, -2], [1, -2, -2]],
451-
[[1, 2, -2], [1, 2, -2]],
449+
[[1, -2, -2], [-2, -2, -2]],
450+
[[-2, -2, -2], [1, -2, -2]],
451+
[[1, -2, -2], [2, -2, -2]],
452452
[[1, 2, 3], [2, 3, -2]],
453-
[[1, -2, -2], [1, -2, -2]],
454-
[[2, -2, -2], [1, -2, -2]],
453+
[[-2, -2, -2], [-2, -2, -2]],
454+
[[-2, -2, -2], [1, -2, -2]],
455455
[[1, -2, -2], [-1, -2, -2]],
456456
[[2, -2, -2], [2, -2, -2]],
457-
[[1, -2, -2], [-2, -2, -2]],
458457
[[-2, -2, -2], [-2, -2, -2]],
459-
[[1, -2, -2], [1, -2, -2]],
458+
[[-2, -2, -2], [-2, -2, -2]],
459+
[[-2, -2, -2], [1, -2, -2]],
460460
]
461461
nt.assert_array_equal(ds.call_LAA.values, call_LAA)
462462

463463
def test_call_LPL(self, ds):
464464
call_LPL = [
465465
[
466466
[100, 0, 105, -2, -2, -2, -2, -2, -2, -2],
467-
[0, 100, 200, -2, -2, -2, -2, -2, -2, -2],
467+
[0, -2, -2, -2, -2, -2, -2, -2, -2, -2],
468468
],
469469
[
470-
[0, 100, 200, -2, -2, -2, -2, -2, -2, -2],
470+
[0, -2, -2, -2, -2, -2, -2, -2, -2, -2],
471471
[154, 22, 0, -2, -2, -2, -2, -2, -2, -2],
472472
],
473473
[
474-
[1002, 55, 1002, 0, 55, 1002, -2, -2, -2, -2],
475-
[154, 154, 0, 154, 102, 102, -2, -2, -2, -2],
474+
[1002, 55, 1002, -2, -2, -2, -2, -2, -2, -2],
475+
[154, 154, 102, -2, -2, -2, -2, -2, -2, -2],
476476
],
477477
[
478478
[-1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
479479
[-1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
480480
],
481481
[
482-
[30, 30, 30, -2, -2, -2, -2, -2, -2, -2],
483-
[30, 60, 0, -2, -2, -2, -2, -2, -2, -2],
482+
[30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
483+
[30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
484484
],
485485
[
486486
[0, 30, -2, -2, -2, -2, -2, -2, -2, -2],
@@ -495,12 +495,12 @@ def test_call_LPL(self, ds):
495495
[10, 40, 60, -2, -2, -2, -2, -2, -2, -2],
496496
],
497497
[
498-
[30, 30, 30, -2, -2, -2, -2, -2, -2, -2],
499-
[30, -1, 0, -2, -2, -2, -2, -2, -2, -2],
498+
[30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
499+
[30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
500500
],
501501
[
502-
[-1, -1, -1, -2, -2, -2, -2, -2, -2, -2],
503-
[-1, -1, -1, -2, -2, -2, -2, -2, -2, -2],
502+
[-1, -2, -2, -2, -2, -2, -2, -2, -2, -2],
503+
[-1, -2, -2, -2, -2, -2, -2, -2, -2, -2],
504504
],
505505
[
506506
[-1, -1, -2, -2, -2, -2, -2, -2, -2, -2],
@@ -637,107 +637,12 @@ def test_call_AD(self, ds):
637637
nt.assert_array_equal(ds.call_AD.values, call_AD)
638638

639639
def test_call_LAA(self, ds):
640-
call_LAA = [
641-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
642-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
643-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
644-
[[1, 2, -2, -2], [1, 2, -2, -2], [1, 2, -2, -2]],
645-
[[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
646-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
647-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
648-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
649-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
650-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
651-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
652-
[[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
653-
[[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
654-
[[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
655-
[[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
656-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
657-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
658-
[[1, 2, -2, -2], [1, 2, -2, -2], [1, 2, -2, -2]],
659-
[[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
660-
[[1, 2, -2, -2], [1, 2, -2, -2], [1, 2, -2, -2]],
661-
[[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
662-
[[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
663-
[[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
664-
]
640+
# All the genotypes are 0/0
641+
call_LAA = np.full((23, 3, 1), -2)
665642
nt.assert_array_equal(ds.call_LAA.values, call_LAA)
666643

667644
def test_call_LPL(self, ds):
668-
# fmt: off
669-
call_LPL = [
670-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
671-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
672-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
673-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
674-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
675-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
676-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
677-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
678-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
679-
[[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
680-
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
681-
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
682-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
683-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
684-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]], # noqa: E501
685-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
686-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
687-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
688-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
689-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
690-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
691-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
692-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
693-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
694-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
695-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
696-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
697-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
698-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
699-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
700-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
701-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
702-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
703-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
704-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
705-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
706-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
707-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
708-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
709-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
710-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
711-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
712-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
713-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
714-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]], # noqa: E501
715-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
716-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
717-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
718-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
719-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
720-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
721-
[[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
722-
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
723-
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
724-
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
725-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
726-
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
727-
[[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
728-
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
729-
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
730-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
731-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
732-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]], # noqa: E501
733-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
734-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
735-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
736-
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
737-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
738-
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]]
739-
]
740-
# fmt: on
645+
call_LPL = np.tile([0, -2, -2], (23, 3, 1))
741646
nt.assert_array_equal(ds.call_LPL.values, call_LPL)
742647

743648
def test_call_PID(self, ds):

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