def test_add_tag_values_nullValues(self):
line = self.entab("CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|JQ_DP:{}{}|X:.|Y:.\n".format(summarize_caller.JQ_SUMMARY_TAG, summarize_caller.JQ_PASSED))
processedVcfRecord = VcfRecord.parse_record(line, ["SA", "SB"])
tag = summarize_caller._SamplesPassed()
tag.add_tag_values(processedVcfRecord)
expected = self.entab("CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO;{}{}=0|JQ_DP:{}{}|X:.|Y:.\n".format(summarize_caller.JQ_SUMMARY_TAG, summarize_caller.JQ_SAMPLES_PASSED, summarize_caller.JQ_SUMMARY_TAG, summarize_caller.JQ_PASSED))
self.assertEquals(expected, processedVcfRecord.text())
def test_add_tag_values_nonePassed(self):
line = self.entab("CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|JQ_DP:{}{}|X:0|Y:0\n".format(summarize_caller.JQ_SUMMARY_TAG, summarize_caller.JQ_PASSED))
vcf_record = VcfRecord.parse_record(line, ["SA", "SB"])
tag = summarize_caller._SamplesPassed()
tag.add_tag_values(vcf_record)
info_tag = summarize_caller.JQ_SUMMARY_TAG + summarize_caller.JQ_SAMPLES_PASSED
self.assertIn(info_tag, vcf_record.info_dict)
self.assertEquals("0", vcf_record.info_dict[info_tag])
def test_metaheader(self):
split_metaheader = summarize_caller._SamplesPassed().metaheader.split("\n")
self.assertEquals('##INFO=<ID={}{},Number=1,Type=Integer,Description="Count of samples where a variant caller passed the filter in any of the Jacquard tagged VCFs">'.format(summarize_caller.JQ_SUMMARY_TAG, summarize_caller.JQ_SAMPLES_PASSED),
split_metaheader[0])