def test_add_tag_values_oneValueReturnsNull(self):
tag = summarize_caller._DepthAverageTag()
sample_tag_values = {"SA": {"JQ_foo_DP": "."}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals(".", record.sample_tag_values["SA"][DepthAverageTagTestCase._TAG_ID])
def test_add_tag_values_rounds(self):
tag = summarize_caller._DepthAverageTag()
sample_tag_values = {"SA": {"JQ_foo_DP": "0", "JQ_bar_DP": "3"}}
record = VcfRecord("CHROM", "POS", "REF", "ALT",
sample_tag_values=sample_tag_values)
tag.add_tag_values(record)
self.assertEquals("1.5", record.sample_tag_values["SA"][DepthAverageTagTestCase._TAG_ID])
def test_add_tag_values_inconsistentMultAlt(self):
tag = summarize_caller._DepthAverageTag()
sample_tag_values = {"SA": {"JQ_foo_DP": "0,0.1", "JQ_bar_DP": "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._DepthAverageTag().metaheader.split("\n")
self.assertEquals('##FORMAT=<ID={}DP_AVERAGE,Number=1,Type=Float,Description="Average depth across recognized variant callers that reported depth for this sample-locus; rounded to integer [round(average(JQ_*_DP))].">'.format(summarize_caller.JQ_SUMMARY_TAG),
split_meta_header[0])
