def test_add_tag_value_validIndelAltEdgecaseNoFilter(self): record = vcf.VcfRecord("chr1", "42", "A", "ACGTNacgtn,*.", vcf_filter="PASS") translate._ExcludeMissingAlt().add_tag_values(record) self.assertEquals("PASS", record.filter)
def test_add_tag_value_missingAltBothNoFilter(self): record = vcf.VcfRecord("chr1", "42", "A", ".*", vcf_filter="PASS") translate._ExcludeMissingAlt().add_tag_values(record) self.assertEquals("PASS", record.filter)
def test_add_tag_value_missingAltNullReplacesFilter(self): record = vcf.VcfRecord("chr1", "42", "A", ".", vcf_filter="PASS") translate._ExcludeMissingAlt().add_tag_values(record) self.assertEquals("JQ_EXCLUDE_MISSING_ALT", record.filter)
def test_metaheader(self): self.assertEquals('##FILTER=<ID=JQ_EXCLUDE_MISSING_ALT,Description="The alternate allele is missing for this variant record.">', translate._ExcludeMissingAlt().metaheader)
def test_metaheader(self): self.assertEquals( '##FILTER=<ID=JQ_EXCLUDE_MISSING_ALT,Description="The alternate allele is missing for this variant record.">', translate._ExcludeMissingAlt().metaheader)