88485cfa7f13affa28ec5765fe9b2db90cce42b6
markd
  Tue Dec 8 21:02:15 2020 -0800
hgPcr working

diff --git src/hg/lib/coordConv.c src/hg/lib/coordConv.c
index 7764dea..c245ad7 100644
--- src/hg/lib/coordConv.c
+++ src/hg/lib/coordConv.c
@@ -253,36 +253,36 @@
 
 
 if(seq == NULL || db == NULL)
     errAbort("coordConv::doDnaAlignment() - dnaSeq and/or db can't be NULL.");
 if(strlen(seq->dna) != seq->size)
     errAbort("coordConv::doDnaAlignment() - there seems to be something fishy about %s: the size doesn't equal the length", seq->name);
 /* if there are too many n's it can cause the blat server to hang */
 if(strstr(seq->dna, "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn") )
   return NULL; 
 makeTempName(&pslTn,"ccR", ".psl");
 f = mustOpen(pslTn.forCgi, "w");
 gvo = gfOutputPsl(920, FALSE, FALSE, f, FALSE, FALSE);
 gfOutputHead(gvo, f);
 
 /* align to genome, both strands */
-struct gfConnection *conn = gfConnect(blatHost, port, FALSE);
-gfAlignStrand(conn, nibDir, seq, FALSE, 20, tFileCache, gvo, NULL, NULL);
+struct gfConnection *conn = gfConnect(blatHost, port, NULL, NULL);
+gfAlignStrand(conn, nibDir, seq, FALSE, 20, tFileCache, gvo);
 reverseComplement(seq->dna, seq->size);
 gfDisconnect(&conn);
-conn = gfConnect(blatHost, port, FALSE);
-gfAlignStrand(conn, nibDir, seq, TRUE, 20 , tFileCache, gvo, NULL, NULL);
+conn = gfConnect(blatHost, port, NULL, NULL);
+gfAlignStrand(conn, nibDir, seq, TRUE, 20 , tFileCache, gvo);
 gfDisconnect(&conn);
 gfOutputQuery(gvo, f);
 carefulClose(&f);
 pslList = pslLoadAll(pslTn.forCgi);
 remove(pslTn.forCgi);
 gfOutputFree(&gvo);
 return pslList;
 }
 
 void getAlignmentsForSeqs(struct coordConvRep *ccr, char *blatHost, char *port, char *nibDir)
 /* Do alignments for the the dnaSeqs in a coordConvRep */
 {
 struct hash *tFileCache = gfFileCacheNew();
 if(!(ccr->midSeq && ccr->upSeq && ccr-> downSeq))
     errAbort("coordConv::getAlignmentsForSeqs() - can't have any NULL dnaSeqs.");