b48da38d4aa8dcb9dc75cc1a37b528a5b42b3265
max
  Thu Jul 18 03:41:35 2024 -0700
adding user suggested dash fix, refs #34121

diff --git src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
index 3f0f45e..9b756bf 100755
--- src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
+++ src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
@@ -314,31 +314,31 @@
             continue
         score = str(determineScore(tpmCutoffs, float(splitLine[-3])))
         if autoSql:
             #skip the 4th field since we recalculated it
             #need a different ordering to account for possible extraFields
             bedLine = "\t".join(splitLine[:4] + [score] + splitLine[5:7] + splitLine[-2:] + splitLine[7:-3]) + "\n"
         else:
             #skip the 4th field since we recalculate it
             bedLine = "\t".join(splitLine[:4] + [score] + splitLine[5:7] + splitLine[8:]) + "\n"
 
         bedFile.write(bedLine)
 
     # Run Max's indexing script: TODO: add verbose options
     indexedBedFile = tempfile.NamedTemporaryFile(mode="w+", bufsize=1)
     cmd = "bedJoinTabOffset " + options.matrixFile.name + " " + bedFile.name + " " + indexedBedFile.name
-    if not options.verbose: cmd += " &>/dev/null"
+    if not options.verbose: cmd += " 2>&1 >/dev/null"
     os.system(cmd)
 
     # Prepend the bed info to the start of the file.
     cmd = "echo '" + bedInfo + "' > " + options.outputFile.name
     os.system(cmd)
 
     # any extra fields must come after the fields added by bedJoinTabOffset
     if autoSql:
         reorderedBedFile = tempfile.NamedTemporaryFile(mode="w+", bufsize=1)
         # first print the standard bed6+3 barChart fields
         # then print the two fields added by bedJoinTabOffset
         # then any extra fields at the end:
         cmd = "awk -F'\\t' -v \"OFS=\\t\" '" + \
                 "{for (i = 1; i < 10; i++) {if (i > 1) printf \"\\t\"; printf \"%s\", $i;}; " + \
                 "for (i = NF-1; i <= NF; i++) {printf \"\\t%s\", $i;} " + \