multithread for samtools sort in sga-align

jts · Aug 8, 2019 · 56fb39d · 56fb39d
1 parent af73db6
commit 56fb39d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/bin/sga-align b/src/bin/sga-align
@@ -49,9 +49,9 @@ def runMerge(inFiles, outFile):
     runCmd(cmd)
 
 def runSort(inFile, outFile):
-
+    global threads
     (outPrefix, fileExtension) = os.path.splitext(outFile)
-    cmd = "samtools sort %s -o %s.bam" % (inFile, outPrefix)
+    cmd = "samtools sort -@ %d %s -o %s.bam" % (threads, inFile, outPrefix)
     runCmd(cmd)
 
     #cmd = "samtools index %s" % (outFile)