def test_add_tag_value_validIndelRefEdgecaseNoFilter(self):
record = vcf.VcfRecord("chr1",
"42",
"ACGTNacgtn",
"C",
vcf_filter="PASS")
translate._ExcludeMalformedRef().add_tag_values(record)
self.assertEquals("PASS", record.filter)
def test_add_tag_value_invalidIndelReplacesFilter(self):
record = vcf.VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="PASS")
translate._ExcludeMalformedRef().add_tag_values(record)
self.assertEquals("JQ_EXCLUDE_MALFORMED_REF", record.filter)
def test_add_tag_value_validIndelRefEdgecaseNoFilter(self):
record = vcf.VcfRecord("chr1", "42", "ACGTNacgtn", "C", vcf_filter="PASS")
translate._ExcludeMalformedRef().add_tag_values(record)
self.assertEquals("PASS", record.filter)
def test_metaheader(self):
self.assertEquals('##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">',
translate._ExcludeMalformedRef().metaheader)
def test_add_tag_value_invalidIndelReplacesFilter(self):
record = vcf.VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="PASS")
translate._ExcludeMalformedRef().add_tag_values(record)
self.assertEquals("JQ_EXCLUDE_MALFORMED_REF", record.filter)
def test_metaheader(self):
self.assertEquals(
'##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">',
translate._ExcludeMalformedRef().metaheader)
