c7653932e0efd97ebcb24e459434fbbeb28a1e97
kuhn
  Thu May 29 08:41:03 2014 -0700
added 54844 to chromsizes file as suggested by Jonathan.  Refs #13331
diff --git src/utils/qa/bamToBigWig.csh src/utils/qa/bamToBigWig.csh
index 44a2bba..013a804 100755
--- src/utils/qa/bamToBigWig.csh
+++ src/utils/qa/bamToBigWig.csh
@@ -1,60 +1,60 @@
 #!/bin/tcsh
 
 ###############################################
 # 
 #  05-22-2014
 #  Robert Kuhn
 #
 #  convert a BAM file to bigWig
 # 
 ###############################################
 
 onintr cleanup
 
 set db=""
 set bamFile=""
 set bwFile=""
 
 
 if ( $#argv == 0 || $#argv > 4 ) then
   # no command line args
   echo
   echo "  convert a BAM file into a bigWig"
   echo "  requires bedtools"
   echo
   echo "    usage:  db  in.bam  out.bw  [splitByStrand]"
   echo "      where splitByStrand makes two output files"
   echo
   exit
 endif
 
 set db=$argv[1]
 set bamFile=$argv[2]
 set bigWigFile=$argv[3]
 
 # if bigwig file has .bw on the end, remove so can add plus/minus before .bw
 set bigWigFile=`echo $bigWigFile | sed s/.bw\$//`
 
-fetchChromSizes $db > $db.chromsizes 
+fetchChromSizes $db > $db.chromsizes$$
 
 if ( $#argv == 4 ) then
   if ( $argv[4] == "splitByStrand" ) then
     bamToBedGraph.csh $db $bamFile $bamFile.bedgraph splitByStrand
-    bedGraphToBigWig $bamFile.bedgraph.plus $db.chromsizes $bigWigFile.plus.bw
-    bedGraphToBigWig $bamFile.bedgraph.minus $db.chromsizes $bigWigFile.minus.bw
+    bedGraphToBigWig $bamFile.bedgraph.plus  $db.chromsizes$$ $bigWigFile.plus.bw
+    bedGraphToBigWig $bamFile.bedgraph.minus $db.chromsizes$$ $bigWigFile.minus.bw
   else
     echo
     echo '  4th argument can only be:  "splitByStrand"'
     $0
     exit
   endif
 else
   bamToBedGraph.csh $db $bamFile $bamFile.bedgraph
-  bedGraphToBigWig $bamFile.bedgraph $db.chromsizes $bigWigFile.bw
+  bedGraphToBigWig $bamFile.bedgraph $db.chromsizes$$ $bigWigFile.bw
 endif
 
 cleanup:
-rm -f $db.chromsizes 
+rm -f $db.chromsizes$$
 rm -f $bamFile.bedgraph.plus
 rm -f $bamFile.bedgraph.minus
 rm -f $bamFile.bedgraph