src/hg/tcga/scripts/segToBed15.py 1.2

Index: src/hg/tcga/scripts/segToBed15.py
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/tcga/scripts/segToBed15.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/tcga/scripts/segToBed15.py	6 Aug 2009 22:56:50 -0000	1.1
+++ src/hg/tcga/scripts/segToBed15.py	18 Sep 2009 23:40:43 -0000	1.2
@@ -17,9 +17,9 @@
         sample = data[0]
         chrom = "chr" + data[1]
         start = int(data[2])
         stop = int(data[3])
-        val = float(data[5])
+        val = float(data[4])
 
         if sample not in segData:
             segData[sample] = {}
 
@@ -118,9 +118,13 @@
             s += '1000' + '\t' + '+' + '\t' + start + '\t' + stop + '\t'
             s += '0' + '\t' + '1' + '\t' + length + '\t' + '0,' + '\t' + numSamples + '\t'
             vals = []
             for sample in samples:
+                if c in mapped[sample]:
                 val = mapped[sample][c].vals[i]
+                else:
+                    val = MISSING_VAL
+                    
                 if val == MISSING_VAL:
                     valStr = ''
                 else:
                     valStr = str(val)