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_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_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_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)
