re-enabled multiprocessing module for 1 cpu case

WGLab · Aug 3, 2021 · 217427d · 217427d
1 parent 1b95a41
commit 217427d
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 17 deletions.
diff --git a/scripts/NanoCaller.py b/scripts/NanoCaller.py
@@ -10,10 +10,7 @@
 def run(args):
     import snpCaller, indelCaller
 
-    if args.cpu==1:
-        pool=None
-    else:
-        pool = mp.Pool(processes=args.cpu)
+    pool = mp.Pool(processes=args.cpu)
 
     if not args.output:
         args.output=os.getcwd()
@@ -136,9 +133,8 @@ def run(args):
             final_path=os.path.join(args.output,'%s.final.vcf.gz' %args.prefix)
             run_cmd('bcftools concat %s.phased.vcf.gz %s.vcf.gz -a -d all |bgziptabix %s' %(snp_vcf, indel_vcf, final_path))
 
-    if pool:
-        pool.close()
-        pool.join()
+    pool.close()
+    pool.join()
 
 if __name__ == '__main__':
 

diff --git a/scripts/indelCaller.py b/scripts/indelCaller.py
@@ -95,11 +95,7 @@ def test_model(params,pool):
             d['end']=min(end,mbase+50000)
             in_dict_list.append(d)
 
-        if params['cpu']==1:
-            result=map(get_indel_testing_candidates, in_dict_list)
-
-        else:
-            result=pool.imap_unordered(get_indel_testing_candidates, in_dict_list)
+        result=pool.imap_unordered(get_indel_testing_candidates, in_dict_list)
 
         total_regions=len(in_dict_list)
         completed=0

diff --git a/scripts/snpCaller.py b/scripts/snpCaller.py
@@ -117,11 +117,7 @@ def test_model(params,pool):
             d['end']=min(end,mbase+200000)
             in_dict_list.append(d)
 
-        if params['cpu']==1:
-            result=map(get_snp_testing_candidates, in_dict_list)
-
-        else:
-            result=pool.imap_unordered(get_snp_testing_candidates, in_dict_list)
+        result=pool.imap_unordered(get_snp_testing_candidates, in_dict_list)
 
         total_regions=len(in_dict_list)
         completed=0