def test_SomaticTagFilterMutectCalls_metaheaders(self):
vcf_reader = MockVcfReader(metaheaders=[
"##foo", "##MuTect=123", '##FORMAT=<ID=FA,...>',
"##source=FilterMutectCalls"
])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
metaheaders = mutect_vcf_reader.metaheaders
self.assertIn(mutect._SomaticTagFilterMutectCalls().metaheader,
metaheaders)
def test_filterPassSomeSamplesPhasedVariants(self):
tag = mutect._SomaticTagFilterMutectCalls()
line = 'CHROM^POS^ID^REF^ALT^QUAL^PASS^INFO^F1:F2:F3:GT^SA.1:SA.2:SA.3:0|0^SB.1:SB.2:SB.3:0|1\n'.replace(
'^', '\t')
expected = 'CHROM^POS^ID^REF^ALT^QUAL^PASS^INFO^F1:F2:F3:GT:{0}HC_SOM^SA.1:SA.2:SA.3:0|0:0^SB.1:SB.2:SB.3:0|1:1\n'\
.replace('^', '\t')\
.format(mutect.JQ_MUTECT_TAG)
processedVcfRecord = vcf.VcfRecord.parse_record(line, ["SA", "SB"])
tag.add_tag_values(processedVcfRecord)
self.assertEquals(expected, processedVcfRecord.text())
def test_filterPassSomeSamplesVariants(self):
tag = mutect._SomaticTagFilterMutectCalls()
line = self.entab(\
'CHROM|POS|ID|REF|ALT|QUAL|PASS|INFO|F1:F2:F3:GT|SA.1:SA.2:SA.3:0/0|SB.1:SB.2:SB.3:0/1\n')
expected = self.entab(\
'CHROM|POS|ID|REF|ALT|QUAL|PASS|INFO|F1:F2:F3:GT:{0}HC_SOM|SA.1:SA.2:SA.3:0/0:0|SB.1:SB.2:SB.3:0/1:1\n'\
).format(mutect.JQ_MUTECT_TAG)
processedVcfRecord = vcf.VcfRecord.parse_record(line, ["SA", "SB"])
tag.add_tag_values(processedVcfRecord)
self.assertEquals(expected, processedVcfRecord.text())
def test_filterFailNotSomatic(self):
tag = mutect._SomaticTagFilterMutectCalls()
line = self.entab(\
'CHROM|POS|ID|REF|ALT|QUAL|filter_failed|INFO|F1:F2:F3|SA.1:SA.2:SA.3|SB.1:SB.2:SB.3\n')
expected = self.entab(\
'CHROM|POS|ID|REF|ALT|QUAL|filter_failed|INFO|F1:F2:F3:{0}HC_SOM|SA.1:SA.2:SA.3:0|SB.1:SB.2:SB.3:0\n'\
).format(mutect.JQ_MUTECT_TAG)
processedVcfRecord = vcf.VcfRecord.parse_record(line, ["SA", "SB"])
tag.add_tag_values(processedVcfRecord)
self.assertEquals(expected, processedVcfRecord.text())
def test_filterPassMissingGenotype(self):
tag = mutect._SomaticTagFilterMutectCalls()
line = self.entab(\
'chrQ|42|ID|A|G|QUAL|PASS|INFO|F1:F2:F3|SA.1:SA.2:SA.3|SB.1:SB.2:SB.3\n')
expected = self.entab(\
'chrQ|42|ID|A|G|QUAL|PASS|INFO|F1:F2:F3:{0}HC_SOM|SA.1:SA.2:SA.3:0|SB.1:SB.2:SB.3:0\n'\
).format(mutect.JQ_MUTECT_TAG)
processedVcfRecord = vcf.VcfRecord.parse_record(line, ["SA", "SB"])
self.assertRaisesRegexp(
utils.JQException,
r'Cannot assign somatic status using FilterMutectCalls.*chrQ:42:A:G',
tag.add_tag_values, processedVcfRecord)
def test_metaheader(self):
self.assertEqual(\
'''##FORMAT=<ID={0}HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic
status for MuTect: 0=non-somatic,1=somatic (based on FilterMutectCalls setting
filter to PASS)">'''.replace('\n', '').format(mutect.JQ_MUTECT_TAG),
mutect._SomaticTagFilterMutectCalls().metaheader)