3d71b2793b72fd0f6f4ff1511bb93cf3b6b76497
markd
  Sun Jan 3 14:01:54 2021 -0800
fixed parameter change errors in blatSuite

diff --git src/isPcr/webPcr/webPcr.c src/isPcr/webPcr/webPcr.c
index ebb31b8..1c67b3e 100644
--- src/isPcr/webPcr/webPcr.c
+++ src/isPcr/webPcr/webPcr.c
@@ -1,27 +1,28 @@
 /* webPcr - Web CGI Program For Fast In-Silico PCR Using gfServer. */
 /* Copyright 2004 Jim Kent.  All rights reserved. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "errAbort.h"
 #include "errCatch.h"
 #include "htmshell.h"
 #include "dnautil.h"
 #include "dnaseq.h"
 #include "cheapcgi.h"
+#include "genoFind.h"
 #include "gfPcrLib.h"
 #include "gfWebLib.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "webPcr - Web CGI Program For Fast In-Silico PCR Using gfServer\n"
   "This program is not generally meant to be run from the command line.\n"
   );
 }
 
 struct gfWebConfig *cfg;	/* Our configuration. */
 
 void doGetPrimers(char *fPrimer, char *rPrimer, int maxSize, int minPerfect, int minGood)
@@ -56,32 +57,33 @@
 boolean doPcr(char *fPrimer, char *rPrimer, int maxSize, int minPerfect, int minGood)
 /* Do the PCR, and show results. */
 {
 struct errCatch *errCatch = errCatchNew();
 boolean ok = FALSE;
 
 if (errCatchStart(errCatch))
     {
     struct gfPcrInput *gpi;
     struct gfPcrOutput *gpoList;
     struct gfServerAt *server = gfWebFindServer(cfg->serverList, "wp_db");
 
     AllocVar(gpi);
     gpi->fPrimer = fPrimer;
     gpi->rPrimer = rPrimer;
-    gpoList = gfPcrViaNet(server->host, server->port, 
-    	server->seqDir, gpi, maxSize, minPerfect, minGood);
+    struct gfConnection *conn = gfConnect(server->host, server->port, NULL, NULL);
+    gpoList = gfPcrViaNet(conn, server->seqDir, gpi, maxSize, minPerfect, minGood);
+    gfDisconnect(&conn);
     if (gpoList != NULL)
 	{
 	printf("<TT><PRE>");
 	gfPcrOutputWriteAll(gpoList, "fa", NULL, "stdout");
 	printf("</PRE></TT>");
         ok = TRUE;
 	}
     else
 	errAbort("No matches to %s %s in %s", fPrimer, rPrimer, server->name);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
      {
      warn("%s", errCatch->message->string);
      }