src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c 1.4

Index: src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c	21 Sep 2009 16:57:04 -0000	1.3
+++ src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c	30 Sep 2009 22:29:40 -0000	1.4
@@ -13,8 +13,11 @@
 #include "hgStatsLib.h"
 #include "bioController.h"
 #include "bioPathway.h"
 
+// defined in createTables.c
+
+
 // many of these functions are in bioPathwayLevel.c
 
 void storeEMValsInDb(struct sqlConnection *biConn, char *tableName,
 			  int pathway_id, int cohort_id, int genome_dataset_id, int mrna_dataset_id, struct emParams *emp)
@@ -259,20 +262,21 @@
 {
 if (!ba->analyze)
     return NULL; 
 
-int i,j;
+//int i,j;
 
 fprintf(stdout, "starting em-based pathway analysis.\n");
 
 struct hash *featureHash = createIdHash(biConn, AF_TABLE, "feature_name");
 
-struct slPair *pa, *sp;
+//struct slPair *pa, *sp;
+struct slPair *pa;
 
 int count = 0, numPathways = slCount(spPathways);
 
 // need the dataset ids to pull the em parameters into the right places
-int genome_ds_id, mrna_ds_id;
+int genome_ds_id = -1, mrna_ds_id = -1;
 struct slName *datasetTables;
 
 // get genome and mrna dataset ids
 for(datasetTables = ba->inputTables; datasetTables; datasetTables = datasetTables->next)
@@ -300,14 +304,15 @@
     int feature_id = pd->id;
     count++;
 
 	// skip these pathways cause EM is expensive on them
-	if(feature_id == 8 || feature_id == 20 || feature_id == 27 || feature_id == 28 || feature_id == 29 || feature_id == 30 || feature_id == 32 || feature_id == 40 || feature_id == 42 || feature_id == 55  || feature_id == 56 || feature_id == 58 || feature_id == 59 || feature_id == 72 || feature_id == 74 || feature_id == 92 || feature_id == 99 || feature_id == 104 || feature_id == 106 || feature_id == 112 || feature_id == 121 || feature_id == 132 || feature_id == 135
+	/*if(feature_id == 8 || feature_id == 20 || feature_id == 27 || feature_id == 28 || feature_id == 29 || feature_id == 30 || feature_id == 32 || feature_id == 40 || feature_id == 42 || feature_id == 55  || feature_id == 56 || feature_id == 58 || feature_id == 59 || feature_id == 72 || feature_id == 74 || feature_id == 92 || feature_id == 99 || feature_id == 104 || feature_id == 106 || feature_id == 112 || feature_id == 121 || feature_id == 132 || feature_id == 135
 	   )
 		{
 		fprintf(stderr, "Skipping pathway %d because EM is too expensive.\n",count);
 		continue;
 		}
+	*/
 		
 	// next check to see if we've already run EM on this pathway
 	struct dyString *emResultQuery = dyStringNew(256);
 	dyStringPrintf(emResultQuery, "SELECT * FROM %s WHERE pathway_id = %d AND cohort_id = %d", EM_TABLE, feature_id, ba->cohort_id);