3035fe4b8c8e8ac74f12417dd350e25f11290dd4
braney
  Sun Apr 12 09:42:43 2020 -0700
support RNA genomes by repurposing hgPbOk in dbDb to specify whether the
database is an RNA genome  #25350

diff --git src/hg/hgTracks/wigMafTrack.c src/hg/hgTracks/wigMafTrack.c
index 600aedd..142d47f 100644
--- src/hg/hgTracks/wigMafTrack.c
+++ src/hg/hgTracks/wigMafTrack.c
@@ -2376,30 +2376,32 @@
 for (mi = miList->next, i=1; mi != NULL && mi->db != NULL; mi = mi->next, i++)
     {
     char *line;
 
     line  = lines[i];
     /* TODO: leave lower case in to indicate masking ?
        * NOTE: want to make sure that all sequences are soft-masked
        * if we do this */
     /* HAVE DONE:  David doesn't like lower case by default
      * TODO: casing based on quality values ?? */
     alignSeqToUpperN(line);
     if (complementBases)
         {
 	complement(line, strlen(line));
         }
+    if (genomeIsRna)
+        toRna(line);
     /* draw sequence letters for alignment */
     hvGfxSetClip(hvg, x, y-1, width, mi->height);
 
     /* having these static here will allow the option 'codonDefault'
      * to run rapidly through the display without extra calls to SQL
      * for the same answer over and over.  For other codon modes, it
      * will still need to query the Frames table repeatedly.
      * This was found to speed up dramatically by adding an index to
      * the table:
      * hgsql staAur2 -e 'CREATE INDEX src on multiz369wayFrames (src, bin);'
      */
     static char * extraPrevious = NULL;
     static struct mafFrames *mfList = NULL, *mf;
     static boolean found = FALSE;
     if (framesTable != NULL)