From 02a59384b1e22f97dab3f467edd2ce75370a2e40 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <yossi@fulcrumgenomics.com>
Date: Fri, 19 Jul 2024 11:21:32 -0400
Subject: [PATCH] fix parallelism for osx

---
 src/sniffles/sniffles | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/sniffles/sniffles b/src/sniffles/sniffles
index fcde5ce..9a1fa90 100755
--- a/src/sniffles/sniffles
+++ b/src/sniffles/sniffles
@@ -10,6 +10,7 @@
 #
 import logging
 import logging.config
+import multiprocessing
 from typing import Optional
 
 from sniffles.utils.resmon import ResourceMonitor
@@ -70,6 +71,8 @@ def Sniffles2_Main(processes: list[parallel.SnifflesWorker]):
 
     input_ext = [f.split(".")[-1].lower() for f in config.input]
 
+    # needed for running on osx
+    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))})")