d8a949135724f97cfc92b52111ac223fece3dbf5
markd
  Mon Jun 29 14:53:25 2020 -0700
got entire tree compliing with geneFind changes

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 659413e..1883a66 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -1583,61 +1583,61 @@
 	warn("Sequence %s would take us over the %d letter limit, stopping here.",
 	     seq->name, maxTotalSize);
 	break;
 	}
 
     conn = gfConnectEx(serve->host, serve->port);
 
     if (isTx)
 	{
 	gvo->reportTargetStrand = TRUE;
 	if (isTxTx)
 	    {
 	    if (allGenomes)
 		queryServer(conn, db, seq, "transQuery", xType, TRUE, FALSE, FALSE, seqNumber);
 	    else
-		gfAlignTransTrans(&conn, serve->nibDir, seq, FALSE, 5, tFileCache, gvo, !txTxBoth);
+		gfAlignTransTrans(&conn, serve->nibDir, seq, FALSE, 5, tFileCache, gvo, !txTxBoth, NULL);
 	    if (txTxBoth)
 		{
 		reverseComplement(seq->dna, seq->size);
 		conn = gfConnectEx(serve->host, serve->port);
 		if (allGenomes)
 		    queryServer(conn, db, seq, "transQuery", xType, TRUE, FALSE, TRUE, seqNumber);
 		else
-		    gfAlignTransTrans(&conn, serve->nibDir, seq, TRUE, 5, tFileCache, gvo, FALSE);
+		    gfAlignTransTrans(&conn, serve->nibDir, seq, TRUE, 5, tFileCache, gvo, FALSE, NULL);
 		}
 	    }
 	else
 	    {
 	    if (allGenomes)
 		queryServer(conn, db, seq, "protQuery", xType, TRUE, TRUE, FALSE, seqNumber);
 	    else
-		gfAlignTrans(&conn, serve->nibDir, seq, 5, tFileCache, gvo);
+		gfAlignTrans(&conn, serve->nibDir, seq, 5, tFileCache, gvo, NULL);
 	    }
 	}
     else
 	{
 	if (allGenomes)
 	    queryServer(conn, db, seq, "query", xType, FALSE, FALSE, FALSE, seqNumber);
 	else
-	    gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo);
+	    gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo, NULL);
 	reverseComplement(seq->dna, seq->size);
 	conn = gfConnectEx(serve->host, serve->port);
 	if (allGenomes)
 	    queryServer(conn, db, seq, "query", xType, FALSE, FALSE, TRUE, seqNumber);
 	else
-	    gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo);
+	    gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo, NULL);
 	}
     gfOutputQuery(gvo, f);
     ++seqNumber;
     }
 carefulClose(&f);
 
 if (!allGenomes)
     {
     showAliPlaces(pslTn.forCgi, faTn.forCgi, NULL, serve->db, qType, tType, 
               organism, feelingLucky);
     }
 
 if(!feelingLucky && !allGenomes)
     cartWebEnd();