From 636d7447d15cf4938251cdd81195ed469e4b9123 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Fri, 16 Feb 2024 11:15:13 +0000 Subject: [PATCH] Skip problematic fields in scikit-allel comparison Temporary workaround to get tests to pass before addressing #1195 --- sgkit/tests/io/vcf/test_vcf_scikit_allel.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/sgkit/tests/io/vcf/test_vcf_scikit_allel.py b/sgkit/tests/io/vcf/test_vcf_scikit_allel.py index ef797f6eb..131da41cb 100644 --- a/sgkit/tests/io/vcf/test_vcf_scikit_allel.py +++ b/sgkit/tests/io/vcf/test_vcf_scikit_allel.py @@ -131,15 +131,23 @@ def test_DP_field(shared_datadir, tmpdir): assert_identical(allel_ds, sg_ds) -@pytest.mark.skip("Temporarily disabling test; see #1195") @pytest.mark.parametrize( "vcf_file,allel_exclude_fields,sgkit_exclude_fields,max_alt_alleles", [ - ("sample.vcf.gz", None, None, 3), + # Excluding AA here because of pad-vs-missing data in sckit-allel strings + # https://github.com/pystatgen/sgkit/issues/1195 + ("sample.vcf.gz", ["AA"], ["INFO/AA"], 3), ("mixed.vcf.gz", None, None, 3), # exclude PL since it has Number=G, which is not yet supported + # Excluding PGT and PID here because of pad-vs-missing data in sckit-allel strings + # https://github.com/pystatgen/sgkit/issues/1195 # increase max_alt_alleles since scikit-allel does not truncate genotype calls - ("CEUTrio.20.21.gatk3.4.g.vcf.bgz", ["calldata/PL"], ["FORMAT/PL"], 7), + ( + "CEUTrio.20.21.gatk3.4.g.vcf.bgz", + ["calldata/PL", "calldata/PGT", "calldata/PID"], + ["FORMAT/PL", "FORMAT/PGT", "FORMAT/PID"], + 7, + ), ], ) @pytest.mark.filterwarnings(