def _check_variantcaller(item):
"""Ensure specified variantcaller is a valid choice.
"""
allowed = set(genotype.get_variantcallers().keys() + [None, False])
vcs = item["algorithm"].get("variantcaller", "gatk")
if not isinstance(vcs, (tuple, list)):
vcs = [vcs]
problem = [x for x in vcs if x not in allowed]
if len(problem) > 0:
raise ValueError("Unexpected algorithm 'variantcaller' parameter: %s\n"
"Supported options: %s\n" % (problem, sorted(list(allowed))))
def _check_variantcaller(item):
"""Ensure specified variantcaller is a valid choice.
"""
allowed = set(genotype.get_variantcallers().keys() + [None, False])
vcs = item["algorithm"].get("variantcaller", "gatk")
if not isinstance(vcs, (tuple, list)):
vcs = [vcs]
problem = [x for x in vcs if x not in allowed]
if len(problem) > 0:
raise ValueError("Unexpected algorithm 'variantcaller' parameter: %s\n"
"Supported options: %s\n" % (problem, sorted(list(allowed))))
def _add_filename_details(full_f):
"""Add variant callers and germline information standard CWL filenames.
This is an ugly way of working around not having metadata with calls.
"""
out = {"vrn_file": full_f}
f = os.path.basename(full_f)
for vc in genotype.get_variantcallers().keys() + ["ensemble"]:
if f.find("-%s.vcf" % vc) > 0:
out["variantcaller"] = vc
if f.find("-germline-") >= 0:
out["germline"] = full_f
return out
def _add_filename_details(full_f):
"""Add variant callers and germline information standard CWL filenames.
This is an ugly way of working around not having metadata with calls.
"""
out = {"vrn_file": full_f}
f = os.path.basename(full_f)
for vc in list(genotype.get_variantcallers().keys()) + ["ensemble"]:
if f.find("-%s.vcf" % vc) > 0:
out["variantcaller"] = vc
if f.find("-germline-") >= 0:
out["germline"] = full_f
return out
def _check_variantcaller(item):
"""Ensure specified variantcaller is a valid choice.
"""
allowed = set(genotype.get_variantcallers().keys() + [None, False])
vcs = item["algorithm"].get("variantcaller")
if not isinstance(vcs, dict):
vcs = {"variantcaller": vcs}
for vc_set in vcs.values():
if not isinstance(vc_set, (tuple, list)):
vc_set = [vc_set]
problem = [x for x in vc_set if x not in allowed]
if len(problem) > 0:
raise ValueError("Unexpected algorithm 'variantcaller' parameter: %s\n"
"Supported options: %s\n" % (problem, sorted(list(allowed))))
# Ensure germline somatic calling only specified with tumor/normal samples
if "germline" in vcs or "somatic" in vcs:
paired = vcfutils.get_paired_phenotype(item)
if not paired:
raise ValueError("%s: somatic/germline calling in 'variantcaller' "
"but tumor/normal metadata phenotype not specified" % dd.get_sample_name(item))
def _check_variantcaller(item):
"""Ensure specified variantcaller is a valid choice.
"""
allowed = set(genotype.get_variantcallers().keys() + [None, False])
vcs = item["algorithm"].get("variantcaller")
if not isinstance(vcs, dict):
vcs = {"variantcaller": vcs}
for vc_set in vcs.values():
if not isinstance(vc_set, (tuple, list)):
vc_set = [vc_set]
problem = [x for x in vc_set if x not in allowed]
if len(problem) > 0:
raise ValueError("Unexpected algorithm 'variantcaller' parameter: %s\n"
"Supported options: %s\n" % (problem, sorted(list(allowed))))
# Ensure germline somatic calling only specified with tumor/normal samples
if "germline" in vcs or "somatic" in vcs:
paired = vcfutils.get_paired_phenotype(item)
if not paired:
raise ValueError("%s: somatic/germline calling in 'variantcaller' "
"but tumor/normal metadata phenotype not specified" % dd.get_sample_name(item))
