def _create_validate_config(vrn_file, rm_file, rm_interval_file, rm_genome,
base_dir, data):
"""Create a bcbio.variation configuration input for validation.
"""
if rm_genome:
rm_genome = alignment.get_genome_ref(rm_genome, None, data["dirs"]["galaxy"])[-1]
if rm_genome != data["sam_ref"]:
eval_genome = data["sam_ref"]
else:
eval_genome = None
else:
eval_genome = None
rm_genome = data["sam_ref"]
ref_call = {"file": rm_file, "name": "ref", "type": "grading-ref",
"preclean": True, "prep": True, "remove-refcalls": True}
if rm_interval_file:
ref_call["intervals"] = rm_interval_file
eval_call = {"file": vrn_file, "name": "eval", "remove-refcalls": True}
if eval_genome:
eval_call["ref"] = eval_genome
eval_call["preclean"] = True
eval_call["prep"] = True
exp = {"sample": data["name"][-1],
"ref": rm_genome,
"approach": "grade",
"calls": [ref_call, eval_call]}
if data.get("callable_bam"):
exp["align"] = data["callable_bam"]
intervals = ensemble.get_analysis_intervals(data)
if intervals:
exp["intervals"] = os.path.abspath(intervals)
return {"dir": {"base": base_dir, "out": "work", "prep": "work/prep"},
"experiments": [exp]}
def _create_validate_config(vrn_file, rm_file, rm_interval_file, rm_genome,
base_dir, data):
"""Create a bcbio.variation configuration input for validation.
"""
if rm_genome:
rm_genome = alignment.get_genome_ref(rm_genome, None,
data["dirs"]["galaxy"])[-1]
if rm_genome != data["sam_ref"]:
eval_genome = data["sam_ref"]
else:
eval_genome = None
else:
eval_genome = None
rm_genome = data["sam_ref"]
ref_call = {
"file": rm_file,
"name": "ref",
"type": "grading-ref",
"preclean": True,
"prep": True,
"remove-refcalls": True
}
if rm_interval_file:
ref_call["intervals"] = rm_interval_file
eval_call = {"file": vrn_file, "name": "eval", "remove-refcalls": True}
if eval_genome:
eval_call["ref"] = eval_genome
eval_call["preclean"] = True
eval_call["prep"] = True
exp = {
"sample": data["name"][-1],
"ref": rm_genome,
"approach": "grade",
"calls": [ref_call, eval_call]
}
if data.get("callable_bam"):
exp["align"] = data["callable_bam"]
intervals = ensemble.get_analysis_intervals(data)
if intervals:
exp["intervals"] = os.path.abspath(intervals)
return {
"dir": {
"base": base_dir,
"out": "work",
"prep": "work/prep"
},
"experiments": [exp]
}