def testDuplicateAnnotationMetaData(self):
"""
Tests that the metadata is populated correctly in cases where duplicate annotations are present in the input VCF
file.
"""
inputFilename = os.path.join(*["testdata", "vcf", "example.duplicate_annotation.vcf"])
creator = VcfInputMutationCreator(inputFilename)
md = creator.getMetadata()
self.assertTrue("variant_status" in md, "variant_status field is missing in metadata.")
self.assertTrue("sample_variant_status" in md, "sample_variant_status is missing in metadata.")
def testGetMetaDataWithNoSampleNameExampleVcf(self):
"""
Tests to ensure that the metadata can be retrieved even before createMutations has been called.
"""
inputFilename = os.path.join(*["testdata", "vcf", "example.sampleName.removed.vcf"])
creator = VcfInputMutationCreator(inputFilename)
gtKeys = {'genotype', 'read_depth', 'genotype_quality', 'haplotype_quality', 'q10', 's50', 'samples_number',
'depth_across_samples', 'allele_frequency', 'ancestral_allele', 'dbSNP_membership', 'id', 'qual',
'hapmap2_membership'}
md = creator.getMetadata()
ks = set(md.keys())
diff = gtKeys.symmetric_difference(ks)
self.assertTrue(len(diff) == 0, "Missing keys that should have been seen in the metadata: " + str(diff))
