def compare_single_var(result, bedregion, orig_vars, caller_vars, comparator, inputgt, conf):
"""
Determine a result string for the given result tuple. Not trivial since for NO_MATCH_RESULTS we need to
determine if a simple genotype change will produce a match
:param result: Result tuple produced by a comparator
:param bedregion: Genomic region containing result
:param orig_vars: 'original' (truth) variant set
:param caller_vars: Variants produced by caller
:param comparator: Comparator function
:param inputgt: True variant genotype
:param conf: Configuration
:return:
"""
result_str = result_from_tuple(result)
if result_str == NO_MATCH_RESULT and (inputgt in util.ALL_HET_GTS or inputgt in util.ALL_HOMALT_GTS):
try:
gt_mod_vars = util.set_genotypes(caller_vars, inputgt, bedregion, conf)
bedfile = util.region_to_bedfile(bedregion)
gt_mod_result = comparator(orig_vars, gt_mod_vars, bedfile, conf)
if result_from_tuple(gt_mod_result) == MATCH_RESULT:
if inputgt in util.ALL_HET_GTS:
result_str = ZYGOSITY_EXTRA_ALLELE
else:
result_str = ZYGOSITY_MISSING_ALLELE
except util.GTModException as ex:
logging.warning('Exception while attempting to modify GTs: ' + str(ex))
return result_str
def test_gtmod(self):
orig_vcf = os.path.join(TestUtils.DATA_PATH, TestUtils.COMPLEX_VCF)
orig_vars = ["-".join(line.split("\t")[0:5]) for line in open(orig_vcf) if line[0] != "#"]
mod_vcf = util.set_genotypes(orig_vcf, "0/1", None, None, compress_result=False)
new_vars = ["-".join(line.split("\t")[0:5]) for line in open(mod_vcf) if line[0] != "#"]
self.assertListEqual(orig_vars, new_vars)
for line in open(mod_vcf):
if line[0] == "#":
continue
else:
toks = line.split("\t")
alt = toks[4]
gt = toks[9].split(":")[0]
if alt != util.VCF_MISSING:
self.assertTrue(gt == "0/1")
else:
self.assertTrue(gt == "0")
os.remove(mod_vcf)
