f8fde41647f918a9aa691bd8f187ae814c85168a
hiram
  Tue Apr 2 15:44:59 2013 -0700
saving the existing awk script here so it can be removed from scripts directory refs #9104
diff --git src/hg/genePredToBed/genePredToBed.awk src/hg/genePredToBed/genePredToBed.awk
new file mode 100755
index 0000000..00d8b15
--- /dev/null
+++ src/hg/genePredToBed/genePredToBed.awk
@@ -0,0 +1,32 @@
+#!/usr/bin/awk -f 
+
+#
+# Convert genePred file to a bed file (on stdout)
+#
+BEGIN {
+    FS="\t";
+    OFS="\t";
+}
+{
+    name=$1
+    chrom=$2
+    strand=$3
+    start=$4
+    end=$5
+    cdsStart=$6
+    cdsEnd=$7
+    blkCnt=$8
+
+    delete starts
+    split($9, starts, ",");
+    delete ends
+    split($10, ends, ",");
+    blkStarts=""
+    blkSizes=""
+    for (i = 1; i <= blkCnt; i++) {
+        blkSizes = blkSizes (ends[i]-starts[i]) ",";
+        blkStarts = blkStarts (starts[i]-start) ",";
+    }
+    
+    print chrom, start, end, name, 1000, strand, cdsStart, cdsEnd, 0, blkCnt, blkSizes, blkStarts
+}