def _run_cleanup_pipeline(args):
bam_cleanup = _build_wrapper_command(args)
procs = {}
try:
# Update 'procs' and get the last process in the pipeline
if args.paired_ended:
last_proc = _setup_paired_ended_pipeline(procs, bam_cleanup)
else:
last_proc = _setup_single_ended_pipeline(procs, bam_cleanup)
# Sort, output to stdout (-o)
call_sort = ['samtools', 'sort', "-o", "-", args.temp_prefix]
procs["sort"] = processes.open_proc(call_sort,
stdin=last_proc.stdout,
stdout=processes.PIPE,
close_fds=True)
last_proc.stdout.close()
# Update NM and MD tags; output BAM (-b) to stdout
call_calmd = ['samtools', 'calmd', '-b', '-', args.fasta]
procs["calmd"] = processes.open_proc(call_calmd,
stdin=procs["sort"].stdout)
procs["sort"].stdout.close()
if any(processes.join_procs(procs.values())):
return 1
return 0
except:
for proc in procs.itervalues():
proc.terminate()
raise
def _run_cleanup_pipeline(args):
bam_cleanup = _build_wrapper_command(args)
procs = {}
try:
# Update 'procs' and get the last process in the pipeline
if args.paired_ended:
last_proc = _setup_paired_ended_pipeline(procs, bam_cleanup)
else:
last_proc = _setup_single_ended_pipeline(procs, bam_cleanup)
# Sort, output to stdout (-o)
call_sort = ['samtools', 'sort', "-o", "-", args.temp_prefix]
procs["sort"] = processes.open_proc(call_sort,
stdin=last_proc.stdout,
stdout=processes.PIPE,
close_fds=True)
last_proc.stdout.close()
# Update NM and MD tags; output BAM (-b) to stdout
call_calmd = ['samtools', 'calmd', '-b', '-', args.fasta]
procs["calmd"] = processes.open_proc(call_calmd,
stdin=procs["sort"].stdout)
procs["sort"].stdout.close()
if any(processes.join_procs(procs.values())):
return 1
return 0
except:
for proc in procs.itervalues():
proc.terminate()
raise
def run_batch((args, regions, filename)):
setup = setup_batch(args, regions, filename)
try:
if any(processes.join_procs(setup["procs"].values())):
return None
return filename
except:
# Re-wrap exception with full-traceback; otherwise this information
# is lost when the exception is retrieved in the main process.
raise BatchError(traceback.format_exc())
finally:
cleanup_batch(setup)
def run_batch((args, regions, filename)):
setup = setup_batch(args, regions, filename)
try:
if any(processes.join_procs(setup["procs"].values())):
return None
return filename
except:
# Re-wrap exception with full-traceback; otherwise this information
# is lost when the exception is retrieved in the main process.
raise BatchError(traceback.format_exc())
finally:
cleanup_batch(setup)
