def test_add_tag_values_missingGTTags(self):
tag = summarize_caller._HCGenotypeTag()
sample_tag_values = {"SA": {"JQ_foo_XX": "0/1"}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals(".", record.sample_tag_values["SA"][HCGenotypeTagTestCase._TAG_ID])
def test_prioritize_genotype(self):
tag = summarize_caller._HCGenotypeTag()
self.assertEquals("0/1", tag._prioritize_genotype(["0/1"]))
self.assertEquals("0/1", tag._prioritize_genotype(["0/0", "0/1"]))
self.assertEquals("1/1", tag._prioritize_genotype(["0/0", "1/1"]))
self.assertEquals("1/1", tag._prioritize_genotype(["1/1", "1/1", "0/1"]))
self.assertEquals("0/1", tag._prioritize_genotype(["1/1", "0/1", "0/1"]))
self.assertEquals("0/1", tag._prioritize_genotype(["0/1", "0/2"]))
def test_metaheader(self):
self.assertEquals('##FORMAT=<ID={}HC_GT,Number=1,Type=String,Description="High confidence consensus genotype (inferred from JQ_*_GT and JQ_*_CALLER_PASSED). Majority rules; ties go to the least unusual variant (0/1>0/2>1/1). Variants which failed their filter are ignored.">'.format(summarize_caller.JQ_SUMMARY_TAG),
summarize_caller._HCGenotypeTag().metaheader)
