src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.10

Index: src/hg/bedItemOverlapCount/bedItemOverlapCount.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/bedItemOverlapCount/bedItemOverlapCount.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 4 -r1.9 -r1.10
--- src/hg/bedItemOverlapCount/bedItemOverlapCount.c	13 Mar 2009 05:22:46 -0000	1.9
+++ src/hg/bedItemOverlapCount/bedItemOverlapCount.c	6 Apr 2009 18:40:21 -0000	1.10
@@ -18,11 +18,17 @@
 //static char *strand = (char *)NULL;	/* strand to process, default +	*/
 		/* this is not implemented, the user can filter + and - */
 
 static struct hash *chromHash = NULL;
+static char *host = NULL;
+static char *user = NULL;
+static char *password = NULL;
 
 /* command line option specifications */
 static struct optionSpec optionSpecs[] = {
+    {"host", OPTION_STRING},
+    {"user", OPTION_STRING},
+    {"password", OPTION_STRING},
     {"strand", OPTION_STRING},
     {NULL, 0}
 };
 
@@ -38,9 +44,12 @@
   " sort -k1,1 -k2,2n bedFile.bed \\\n"
   "     | bedItemOverlapCount [options] <database> stdin \\\n"
   "         | wigEncode stdin data.wig data.wib\n"
   "options:\n"
-  "   (none at this time - you will want to separate your + and - strand\n"
+  "   -host\tmysql host\n"
+  "   -user\tmysql user\n"
+  "   -password\tmysql password\n\n"
+  "\tYou will want to separate your + and - strand\n"
   "\titems before sending into this program as it only looks at\n"
   "\tthe chrom, start and end columns of the bed file.\n"
   "\tIt wants a <database> connection to lookup chrom sizes for a sanity\n"
   "\tcheck of the incoming data.  This should be redone to take a chrom.sizes\n"
@@ -54,14 +63,23 @@
 static struct hash *loadAllChromInfo(char *database, unsigned *largest)
 /* Load up all chromosome infos, return largest one if asked to do so. */
 {
 struct chromInfo *el;
-struct sqlConnection *conn = sqlConnect(database);
+struct sqlConnection *conn = NULL;
 struct sqlResult *sr = NULL;
 struct hash *ret;
 char **row;
 unsigned max = 0;
 
+if(host)
+    {
+    conn = sqlConnectRemote(host, user, password, database);
+    }
+else
+    {
+    conn = hAllocConn(database);
+    }
+
 ret = newHash(0);
 
 sr = sqlGetResult(conn, "select * from chromInfo");
 while ((row = sqlNextRow(sr)) != NULL)
@@ -216,8 +234,11 @@
 optionInit(&argc, argv, optionSpecs);
 
 if (argc < 2)
     usage();
+host = optionVal("host", NULL);
+user = optionVal("user", NULL);
+password = optionVal("password", NULL);
 verbose(2, "#\tworking on database: %s\n", argv[1]);
 bedItemOverlapCount(argv[1], argc-2, argv+2);
 return 0;
 }