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fix parallelism for osx #499

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merged 2 commits into from
Aug 13, 2024
Merged

fix parallelism for osx #499

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02a5938
fix parallelism for osx
yfarjoun Jul 19, 2024
b89b496
only change default for "darwin"
yfarjoun Jul 20, 2024
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5 changes: 5 additions & 0 deletions src/sniffles/sniffles
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
#
import logging
import logging.config
import multiprocessing
from typing import Optional

from sniffles.utils.resmon import ResourceMonitor
Expand Down Expand Up @@ -70,6 +71,10 @@ def Sniffles2_Main(processes: list[parallel.SnifflesWorker]):

input_ext = [f.split(".")[-1].lower() for f in config.input]

# needed for running on osx
if sys.platform == "darwin":
multiprocessing.set_start_method("fork")

if len(set(input_ext)) > 1:
util.fatal_error_main(f"Please specify either: A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input. (supplied were: {list(set(input_ext))})")

Expand Down