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

diff --git src/webBlat/webBlat.c src/webBlat/webBlat.c
index 13e8767..ceb002e 100644
--- src/webBlat/webBlat.c
+++ src/webBlat/webBlat.c
@@ -348,61 +348,58 @@
     {
     freez(&seqList->name);
     seqList->name = cloneString("query");
     }
 faWriteAll(faName, seqList);
 
 /* Set up output for blat. */
 f = mustOpen(pslName, "w");
 gvo = gfOutputPsl(0, protQuery, FALSE, f, FALSE, TRUE);
 gvo->includeTargetFile = TRUE;
 
 txServer = isTxType(type);
 server = findServer(txServer);
 
 /* Loop through sequences doing alignments and saving to file. */
-struct gfConnection *conn = gfConnect(server->host, server->port, server->dynGenomeDir != NULL);
+struct gfConnection *conn = gfConnect(server->host, server->port, server->genome, server->dynGenomeDir);
 for (seq = seqList; seq != NULL; seq = seq->next)
     {
     if (txServer)
         {
 	gvo->reportTargetStrand = TRUE;
 	if (protQuery)
 	    {
-	    gfAlignTrans(conn, server->seqDir, seq, 5,
-                         tFileCache, gvo, server->genome, server->dynGenomeDir);
+	    gfAlignTrans(conn, server->seqDir, seq, 5, tFileCache, gvo);
 	    }
 	else
 	    {
 	    boolean isRna = sameWord(type, "RNA");
 	    gfAlignTransTrans(conn, server->seqDir, seq, FALSE, 5,
-                              tFileCache, gvo, isRna, server->genome, server->dynGenomeDir);
+                              tFileCache, gvo, isRna);
 	    if (!isRna)
 	        {
 		reverseComplement(seq->dna, seq->size);
 		gfAlignTransTrans(conn, server->seqDir, seq, TRUE, 5,
-                                  tFileCache, gvo, FALSE, server->genome, server->dynGenomeDir);
+                                  tFileCache, gvo, FALSE);
 		}
 	    }
 	}
     else
         {
-	gfAlignStrand(conn, server->seqDir, seq, FALSE, 16,
-                      tFileCache, gvo, server->genome, server->dynGenomeDir);
+	gfAlignStrand(conn, server->seqDir, seq, FALSE, 16, tFileCache, gvo);
 	reverseComplement(seq->dna, seq->size);
-	gfAlignStrand(conn, server->seqDir, seq, TRUE, 16,
-                      tFileCache, gvo, server->genome, server->dynGenomeDir);
+	gfAlignStrand(conn, server->seqDir, seq, TRUE, 16, tFileCache, gvo);
 	}
     gfOutputQuery(gvo, f);
     }
 gfDisconnect(&conn);
 carefulClose(&f);
 
 /* Display alignment results. */
 aliLines(pslName, faName, server->name, type);
 }
 
 void doGetSeq()
 /* Put up form that asks them to submit sequence. */
 {
 char *qType = NULL;
 char **queryMenu = NULL;