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])