src/hg/instinct/mapProbesToGenes/mapProbesToGenes.c 1.9

Index: src/hg/instinct/mapProbesToGenes/mapProbesToGenes.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/mapProbesToGenes/mapProbesToGenes.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/hg/instinct/mapProbesToGenes/mapProbesToGenes.c	19 Nov 2008 00:34:15 -0000	1.8
+++ src/hg/instinct/mapProbesToGenes/mapProbesToGenes.c	16 Nov 2009 18:37:00 -0000	1.9
@@ -233,9 +233,9 @@
     if (isCgh)
 	{	
 	if (rangeBothStrandOverlap(gene, probe) >0 )
 	    {
-	    if ((probe->chromEnd - probe->chromStart) < 15)
+	    if ((probe->chromEnd - probe->chromStart) < 1)
 		{
 		printf("%s %s %c too short dis=%d\n", 
 		       gene->name, probe->name, gene->strand[0], 
 		       probe->chromEnd- probe->chromStart);
@@ -315,19 +315,32 @@
     return;
 
 char query[512];
 safef(query, sizeof(query),
-      "select * from %s" , table);
+      "select COUNT(*) from %s" , table);
 
 /* "db" is remote database connection, where "refGene" lives */
 struct sqlConnection *conn = hAllocConnProfile("db", database);
 struct sqlResult *sr = sqlGetResult(conn, query);
+int curr = 0;
 
 char **row = NULL;
-struct genePred *gp;
-struct bed *gene;
-while ((row = sqlNextRow(sr)) != NULL)
+row = sqlNextRow(sr);
+unsigned i,count = sqlUnsigned(row[0]);
+sqlFreeResult(&sr);
+
+for(i = 0; i < count; i += 100)
+		{
+		safef(query, sizeof(query),
+				"select * from %s LIMIT %d,100" , table,i);
+				
+		sr = sqlGetResult(conn, query);
+		struct genePred *gp;
+		struct bed *gene;
+		while ((row = sqlNextRow(sr)) != NULL)
     {
+				//printf(">");
+				//fflush(stdout);
     if (row[10])
 	{
 	char *tmp = row[12];
 	row[12] = row[1];
@@ -337,10 +350,20 @@
     gp = genePredLoad(row+1);
     gene = bedFromGenePred(gp);
     genePredFree(&gp);
     reportOverlap(gene, probeList);
+		
+			if((++curr % 100) == 0)
+				{
+				printf(".");
+				fflush(stdout);
     }
-hFreeConn(&conn);
+			}
+		sqlFreeResult(&sr);
+		}
+		printf("done.\n");
+		hFreeConn(&conn);
+
 }
 
 void mapProbesToGenes(char *db, char *table)
 /* mapProbesToGenes - Will maps probes in BED format to overlapping gene(s). */
@@ -359,8 +382,9 @@
     {
     tuple = bedLoadN(row+1, 15);
     slAddHead(&tupleList, tuple);
     }
+sqlFreeResult(&sr);
 
 slReverse(&tupleList);
 overlapWithTable(db, tupleList, "refGene");
 hFreeConn(&conn);