def _get_build_type(fnames, samples, caller):
"""Confirm we should build a gemini database: need gemini in tools_on.
Checks for valid conditions for running a database and gemini or gemini_orig
configured in tools on.
"""
build_type = set()
if any(vcfutils.vcf_has_variants(f)
for f in fnames) and caller not in NO_DB_CALLERS:
for data in samples:
if any([
x in dd.get_tools_on(data) for x in [
"gemini", "gemini_orig", "gemini_allvariants",
"vcf2db_expand"
]
]):
if vcfanno.annotate_gemini(data):
build_type.add("gemini_orig" if "gemini_orig" in
dd.get_tools_on(data) else "gemini")
else:
logger.info(
"Not running gemini, input data not found: %s" %
dd.get_sample_name(data))
else:
logger.info(
"Not running gemini, not configured in tools_on: %s" %
dd.get_sample_name(data))
else:
logger.info("Not running gemini, no samples with variants found: %s" %
(", ".join([dd.get_sample_name(d) for d in samples])))
return build_type
def _get_build_type(fnames, samples, caller):
"""Confirm we should build a gemini database: need gemini in tools_on.
Checks for valid conditions for running a database and gemini or gemini_orig
configured in tools on.
"""
build_type = set()
if any(vcfutils.vcf_has_variants(f)
for f in fnames) and caller not in NO_DB_CALLERS:
for data in samples:
if any([
x in dd.get_tools_on(data) for x in [
"gemini", "gemini_orig", "gemini_allvariants",
"vcf2db_expand"
]
]):
if vcfanno.annotate_gemini(data):
build_type.add("gemini_orig" if "gemini_orig" in
dd.get_tools_on(data) else "gemini")
return build_type