def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for d in joint.square_off(samples, run_parallel):
out.extend(
[[to_single_data(xs)]
for xs in multi.split_variants_by_sample(to_single_data(d))])
samples = out
if variantcaller:
samples = run_parallel("run_rnaseq_ann_filter", samples)
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for data in (to_single_data(xs) for xs in samples):
if "variants" not in data:
data["variants"] = []
data["variants"].append({
"variantcaller": "gatk-haplotype",
"vcf": data["vrn_file_orig"],
"population": {
"vcf": data["vrn_file"]
}
})
data["vrn_file"] = data.pop("vrn_file_orig")
out.append([data])
samples = out
return samples
def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for d in joint.square_off(samples, run_parallel):
out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))])
samples = out
samples = run_parallel("run_rnaseq_ann_filter", samples)
return samples
def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for d in joint.square_off(samples, run_parallel):
out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))])
samples = out
if variantcaller:
samples = run_parallel("run_rnaseq_ann_filter", samples)
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for data in (to_single_data(xs) for xs in samples):
if "variants" not in data:
data["variants"] = []
data["variants"].append({"variantcaller": "gatk-haplotype", "vcf": data["vrn_file_orig"],
"population": {"vcf": data["vrn_file"]}})
data["vrn_file"] = data.pop("vrn_file_orig")
out.append([data])
samples = out
return samples
def split_variants_by_sample(*args):
return multi.split_variants_by_sample(*args)
def split_variants_by_sample(*args):
return multi.split_variants_by_sample(*args)
