def square_batch_region(data, region, bam_files, vrn_files, out_file):
"""Perform squaring of a batch in a supplied region, with input BAMs
"""
from bcbio.variation import sentieon, strelka2
if not utils.file_exists(out_file):
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)
if jointcaller in ["%s-joint" % x for x in SUPPORTED["general"]]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files,
out_file, "square")
elif jointcaller in ["%s-merge" % x for x in SUPPORTED["general"]]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files,
out_file, "merge")
elif jointcaller in ["%s-joint" % x for x in SUPPORTED["gatk"]]:
gatkjoint.run_region(data, region, vrn_files, out_file)
elif jointcaller in ["%s-joint" % x for x in SUPPORTED["gvcf"]]:
strelka2.run_gvcfgenotyper(data, region, vrn_files, out_file)
elif jointcaller in ["%s-joint" % x for x in SUPPORTED["sentieon"]]:
sentieon.run_gvcftyper(vrn_files, out_file, region, data)
else:
raise ValueError("Unexpected joint calling approach: %s." %
jointcaller)
if region:
data["region"] = region
data = _fix_orig_vcf_refs(data)
data["vrn_file"] = out_file
return [data]
def square_batch_region(data, region, bam_files, vrn_files, out_file):
"""Perform squaring of a batch in a supplied region, with input BAMs
"""
if not utils.file_exists(out_file):
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)
if jointcaller in ["freebayes-joint", "platypus-joint"]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files, out_file)
elif jointcaller == "gatk-haplotype-joint":
gatkjoint.run_region(data, region, vrn_files, out_file)
else:
raise ValueError("Unexpected joint calling approach: %s" % jointcaller)
if region:
data["region"] = region
data = _fix_orig_vcf_refs(data)
data["vrn_file"] = out_file
return [data]
def square_batch_region(data, region, bam_files, vrn_files, out_file):
"""Perform squaring of a batch in a supplied region, with input BAMs
"""
if not utils.file_exists(out_file):
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)
if jointcaller in ["%s-joint" % x for x in SUPPORTED["general"]]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files, out_file, "square")
elif jointcaller in ["%s-merge" % x for x in SUPPORTED["general"]]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files, out_file, "merge")
elif jointcaller in ["%s-joint" % x for x in SUPPORTED["gatk"]]:
gatkjoint.run_region(data, region, vrn_files, out_file)
else:
raise ValueError("Unexpected joint calling approach: %s" % jointcaller)
if region:
data["region"] = region
data = _fix_orig_vcf_refs(data)
data["vrn_file"] = out_file
return [data]
def square_batch_region(data, region, bam_files, vrn_files, out_file):
"""Perform squaring of a batch in a supplied region, with input BAMs
"""
supported = ["freebayes", "platypus", "samtools"]
if not utils.file_exists(out_file):
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)
if jointcaller in ["%s-joint" % x for x in supported]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files,
out_file, "square")
elif jointcaller in ["%s-merge" % x for x in supported]:
_square_batch_bcbio_variation(data, region, bam_files, vrn_files,
out_file, "merge")
elif jointcaller == "gatk-haplotype-joint":
gatkjoint.run_region(data, region, vrn_files, out_file)
else:
raise ValueError("Unexpected joint calling approach: %s" %
jointcaller)
if region:
data["region"] = region
data = _fix_orig_vcf_refs(data)
data["vrn_file"] = out_file
return [data]