def piped_bamprep(data, region=None, out_file=None):
"""Perform full BAM preparation using pipes to avoid intermediate disk IO.
Handles recalibration and realignment of original BAMs.
"""
data["region"] = region
if not _need_prep(data):
return [data]
else:
utils.safe_makedir(os.path.dirname(out_file))
if region[0] == "nochrom":
prep_bam = shared.write_nochr_reads(data["work_bam"], out_file,
data["config"])
elif region[0] == "noanalysis":
prep_bam = shared.write_noanalysis_reads(data["work_bam"],
region[1], out_file,
data["config"])
else:
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
_piped_bamprep_region(data, region, out_file, tmp_dir)
prep_bam = out_file
bam.index(prep_bam, data["config"])
data["work_bam"] = prep_bam
return [data]
def piped_bamprep(data, region=None, out_file=None):
"""Perform full BAM preparation using pipes to avoid intermediate disk IO.
Handles de-duplication, recalibration and realignment of original BAMs.
"""
if region[0] == "nochrom":
prep_bam = shared.write_nochr_reads(data["work_bam"], out_file)
elif region[0] == "noanalysis":
prep_bam = shared.write_noanalysis_reads(data["work_bam"], region[1], out_file)
else:
if not utils.file_exists(out_file):
with utils.curdir_tmpdir() as tmp_dir:
_piped_bamprep_region(data, region, out_file, tmp_dir)
prep_bam = out_file
data["work_bam"] = prep_bam
data["regions"]["current"] = region
return [data]
def piped_bamprep(data, region=None, out_file=None):
"""Perform full BAM preparation using pipes to avoid intermediate disk IO.
Handles de-duplication, recalibration and realignment of original BAMs.
"""
utils.safe_makedir(os.path.dirname(out_file))
if region[0] == "nochrom":
prep_bam = shared.write_nochr_reads(data["work_bam"], out_file)
elif region[0] == "noanalysis":
prep_bam = shared.write_noanalysis_reads(data["work_bam"], region[1], out_file)
else:
if not utils.file_exists(out_file):
with utils.curdir_tmpdir() as tmp_dir:
_piped_bamprep_region(data, region, out_file, tmp_dir)
prep_bam = out_file
broad_runner = broad.runner_from_config(data["config"])
broad_runner.run_fn("picard_index", prep_bam)
data["work_bam"] = prep_bam
data["region"] = region
return [data]
def piped_bamprep(data, region=None, out_file=None):
"""Perform full BAM preparation using pipes to avoid intermediate disk IO.
Handles de-duplication, recalibration and realignment of original BAMs.
"""
utils.safe_makedir(os.path.dirname(out_file))
if region[0] == "nochrom":
prep_bam = shared.write_nochr_reads(data["work_bam"], out_file)
elif region[0] == "noanalysis":
prep_bam = shared.write_noanalysis_reads(data["work_bam"], region[1], out_file)
else:
if not utils.file_exists(out_file):
with utils.curdir_tmpdir() as tmp_dir:
_piped_bamprep_region(data, region, out_file, tmp_dir)
prep_bam = out_file
broad_runner = broad.runner_from_config(data["config"])
broad_runner.run_fn("picard_index", prep_bam)
data["work_bam"] = prep_bam
data["region"] = region
return [data]
def piped_bamprep(data, region=None, out_file=None):
"""Perform full BAM preparation using pipes to avoid intermediate disk IO.
Handles recalibration and realignment of original BAMs.
"""
data["region"] = region
if not _need_prep(data):
return [data]
else:
utils.safe_makedir(os.path.dirname(out_file))
if region[0] == "nochrom":
prep_bam = shared.write_nochr_reads(data["work_bam"], out_file, data["config"])
elif region[0] == "noanalysis":
prep_bam = shared.write_noanalysis_reads(data["work_bam"], region[1], out_file, data["config"])
else:
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
_piped_bamprep_region(data, region, out_file, tmp_dir)
prep_bam = out_file
bam.index(prep_bam, data["config"])
data["work_bam"] = prep_bam
return [data]