replaced LC_COLLATE by LC_ALL as the latter overrides the former.

Author: fidelram

deeptools/writeBedGraph.py

@@ -202,7 +202,7 @@ def bedGraphToBigWig(chromSizes, bedGraphPath, bigWigPath, sort=True):
         # temporary file to store sorted bedgraph file
         _file = NamedTemporaryFile(delete=False)
         tempFileName1 = _file.name
-        system("LC_COLLATE=C {} -k1,1 -k2,2n {} > {}".format(sort_cmd,
+        system("LC_ALL=C {} -k1,1 -k2,2n {} > {}".format(sort_cmd,
                                                 bedGraphPath, tempFileName1))
         bedGraphPath = tempFileName1
 
@@ -303,7 +303,7 @@ def writeBedGraph(bamFilesList, outputFileName, fragmentLength,
             print "output file: %s" % (outputFileName)
     else:
         bedGraphToBigWig(
-            chromNamesAndSize, bedGraphFile, outputFileName, False)
+            chromNamesAndSize, bedGraphFile, outputFileName, sort=True)
         if debug:
             print "output file: %s" % (outputFileName)
         os.remove(bedGraphFile)