def clean_chipseq_alignment(data):
aligner = dd.get_aligner(data)
assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2."
if aligner == "bowtie2":
unique_bam = filter_multimappers(dd.get_work_bam(data), data)
data["work_bam"] = unique_bam
return [[data]]
return [[data]]
def clean_chipseq_alignment(data):
aligner = dd.get_aligner(data)
assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2."
if aligner == "bowtie2":
unique_bam = filter_multimappers(dd.get_work_bam(data), data)
data["work_bam"] = unique_bam
return [[data]]
return [[data]]
def clean_chipseq_alignment(data):
config = data["config"]
aligner = config["algorithm"].get("aligner", None)
assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2."
if aligner == "bowtie2":
work_bam = filter_multimappers(data["work_bam"])
data["work_bam"] = work_bam
return [[data]]
def clean_chipseq_alignment(data):
aligner = dd.get_aligner(data)
data["raw_bam"] = dd.get_work_bam(data)
if aligner:
assert aligner == "bowtie2", "ChIP-seq only supported for bowtie2."
unique_bam = filter_multimappers(dd.get_work_bam(data), data)
data["work_bam"] = unique_bam
else:
logger.info("Warning: When BAM file is given as input, bcbio skips multimappers removal."
"If BAM is not cleaned for peak calling, can result in downstream errors.")
return [[data]]
