0edefc9983679d6bbee96ccc100f7d41921def00
braney
  Wed May 28 12:25:49 2025 -0700
working on track visibilities after quickLift

diff --git src/hg/hgConvert/hgConvert.c src/hg/hgConvert/hgConvert.c
index 2c17c955bf3..8ff0c85e9a2 100644
--- src/hg/hgConvert/hgConvert.c
+++ src/hg/hgConvert/hgConvert.c
@@ -344,59 +344,62 @@
 	blockSize = chainTotalBlockSize(chain);
         /* Check if the toDb database exists and if the chromosome
            sequence file (of the hgConvert result) exists in the location
            specified in chromInfo for the toDb. */
 
         boolean chromSeqExists = (sqlDatabaseExists(toDb->name) &&
 				  chromSeqFileExists(toDb->name, chain->qName));
         /* Check if the toDb has active set to 1 in dbDb if the toDb
            database exists.
            If these conditions are met then print position link to
            browser for toDb, otherwise just print position without link. */
         boolean startedAnchor = FALSE;
         if ((hDbIsActive(toDb->name) && chromSeqExists) || startsWith("hub:",toDb->nibPath))
             {
             if (quickChain)
-                printf("<A HREF=\"%s?db=%s&position=%s:%d-%d&quickLift.%d.%s=%d&hideTracks=1%s\">",
-                   hgTracksName(), toDb->name,  chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain, visDy->string);
+                printf("<A HREF=\"%s?db=%s&position=%s:%d-%d&quickLift.%d.%s=%d\">",
+                   hgTracksName(), toDb->name,  chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain);
             else
                 printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\">",
 		   hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd);
             startedAnchor = TRUE;
             }
         else if (sameString(toDb->nibPath, "genark"))
             {
             char *hubUrl = genarkUrl(toDb->name);
             if (hubUrl)
                 {
                 startedAnchor = TRUE;
                 if (quickChain)
                     printf("<A HREF=\"%s?genome=%s&hubUrl=%s&position=%s:%d-%d&quickLift.%d.%s=%d\">",
                        hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain);
                 else
                     printf("<A HREF=\"%s?genome=%s&hubUrl=%s&position=%s:%d-%d\">",
                        hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd);
                 }
             }
 	printf("%s:%d-%d",  chain->qName, qStart+1, qEnd);
         if (startedAnchor)
 	    printf("</A>");
 	printf(" (%3.1f%% of bases, %3.1f%% of span)<BR>\n",
 	    100.0 * blockSize/origSize,
 	    100.0 * (chain->tEnd - chain->tStart) / origSize);
 	}
     }
+if (badList)
+    for(; badList; badList = badList->next)
+        printf("%s %s<BR>", badList->track, badList->type);
 cartWebEnd();
 }
 
 static struct liftOverChain *cleanLiftOverList(struct liftOverChain *list)
 /* eliminate from the list where toDb doesn't exist in dbDb */
 {
 struct liftOverChain *cleanList = NULL;
 struct hash *dbDbHash = hDbDbHash();
 struct liftOverChain *this = NULL;
 struct liftOverChain *next = NULL;
 for (this = list; this != NULL; this = next)
     {
     next = this->next;
     if (hashLookup(dbDbHash, this->toDb))
         slAddHead(&cleanList, this);