src/hg/instinct/bioInt2/bioPathwayLevel.c 1.2

Index: src/hg/instinct/bioInt2/bioPathwayLevel.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioPathwayLevel.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/instinct/bioInt2/bioPathwayLevel.c	20 May 2009 20:34:36 -0000	1.1
+++ src/hg/instinct/bioInt2/bioPathwayLevel.c	20 May 2009 22:42:13 -0000	1.2
@@ -57,9 +57,13 @@
 char *row[2];
 while (lineFileRowTab(lf, row))
     {
     char *name = row[0];
-    double val = atof(row[1]);
+    char *valStr = row[1];
+    if (sameString(valStr, "NA"))
+	continue;
+
+    double val = atof(valStr);
     int entity_id = hashIntValDefault(hash, name, -1);
     if (entity_id == -1)
 	{
 	fprintf(stderr, "entity %s not found\n", name);
@@ -236,9 +240,12 @@
 
 /* Run command (cross fingers!) */
 int ret = system(command);
 if (ret)
-    errAbort("Something went wrong!!");
+    {
+    fprintf(stderr, "Something went wrong!!");
+    return NULL;
+    }
 
 /* read in data from output */
 struct analysisVals *avList = readAnalysisValsFromFile(tmpOutput, pd->entities, sample_id); 
 return avList;