def test_add_tag_values_OnlyCountHCSOMTags(self):
tag = summarize_caller._SomaticTag()
sample_tag_values = {"SA": {"JQ_foo": "1", "JQ_foo_HC_SOM": "1", "JQ_bar_HC_SOM": "1"}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals("2", record.sample_tag_values["SA"][SomaticTagTestCase._TAG_ID])
def test_add_tag_values_missingTag(self):
tag = summarize_caller._SomaticTag()
sample_tag_values = {"SA": {"JQ_foo": "1",}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals(".", record.sample_tag_values["SA"][SomaticTagTestCase._TAG_ID])
def test_metaheader(self):
split_meta_header = summarize_caller._SomaticTag().metaheader.split("\n")
self.assertEqual('##FORMAT=<ID={0}SOM_COUNT,Number=1,Type=Integer,' \
'Description="Count of recognized variant callers ' \
'that reported confident somatic call for this '\
'sample-locus.">'\
.format(summarize_caller.JQ_SUMMARY_TAG), split_meta_header[0])
def test_add_tag_values_inconsistentMultAlt(self):
tag = summarize_caller._SomaticTag()
sample_tag_values = {"SA": {"JQ_foo_HC_SOM": "0,0.1", "JQ_bar_HC_SOM": "0.2"}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
self.assertRaisesRegexp(JQException,
r"Error summarizing values \[.*\] at record \[.*\]",
tag.add_tag_values,
record)
