def test_add_tag_values_nullsDoNotCount(self):
tag = summarize_caller._AlleleFreqRangeTag()
sample_tag_values = {"SA": {"JQ_foo_AF": ".", "JQ_bar_AF": "0.1", "JQ_baz_AF":"0.2"}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals("0.1", record.sample_tag_values["SA"][AlleleFreqRangeTagTestCase._TAG_ID])
def test_add_tag_values_oneValueReturnsNull(self):
tag = summarize_caller._AlleleFreqRangeTag()
sample_tag_values = {"SA": {"JQ_foo_AF": "."}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals(".", record.sample_tag_values["SA"][AlleleFreqRangeTagTestCase._TAG_ID])
def test_add_tag_values_inconsistentMultAlt(self):
tag = summarize_caller._AlleleFreqRangeTag()
sample_tag_values = {"SA": {"JQ_foo_AF": "0,0.1", "JQ_bar_AF": "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)
def test_metaheader(self):
split_meta_header = summarize_caller._AlleleFreqRangeTag().metaheader.split("\n")
self.assertEqual('##FORMAT=<ID={0}AF_RANGE,Number=1,Type=Float,Description="Max(allele frequency) - min (allele frequency) across recognized callers.">'.format(summarize_caller.JQ_SUMMARY_TAG),
split_meta_header[0])
