def test_add_tag_value_validIndelAltEdgecaseNoFilter(self):
record = vcf.VcfRecord("chr1",
"42",
"A",
"ACGTNacgtn,",
vcf_filter="PASS")
translate._ExcludeMalformedAlt().add_tag_values(record)
self.assertEquals("PASS", record.filter)
def test_add_tag_value_missingAltBothReplacesFilter(self):
record = vcf.VcfRecord("chr1", "42", "A", ".*", vcf_filter="PASS")
translate._ExcludeMalformedAlt().add_tag_values(record)
self.assertEquals("JQ_EXCLUDE_MALFORMED_ALT", record.filter)
def test_add_tag_value_validIndelAltEdgecaseNoFilter(self):
record = vcf.VcfRecord("chr1", "42", "A", "ACGTNacgtn,", vcf_filter="PASS")
translate._ExcludeMalformedAlt().add_tag_values(record)
self.assertEquals("PASS", record.filter)
def test_metaheader(self):
self.assertEquals('##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">',
translate._ExcludeMalformedAlt().metaheader)
def test_add_tag_value_missingAltBothReplacesFilter(self):
record = vcf.VcfRecord("chr1", "42", "A", ".*", vcf_filter="PASS")
translate._ExcludeMalformedAlt().add_tag_values(record)
self.assertEquals("JQ_EXCLUDE_MALFORMED_ALT", record.filter)
def test_metaheader(self):
self.assertEquals(
'##FILTER=<ID=JQ_EXCLUDE_MALFORMED_ALT,Description="The the format of the alternate allele value for this variant record does not comply with VCF standard.">',
translate._ExcludeMalformedAlt().metaheader)
