2b99386b970fed3608557122446f987004c69ab5
braney
  Fri Oct 7 12:58:17 2011 -0700
fix a bug that only showed up in building the CDS FASTA alignments for rn4 RGD genes
diff --git src/hg/lib/mafGene.c src/hg/lib/mafGene.c
index 7a03dbc..b01a696 100644
--- src/hg/lib/mafGene.c
+++ src/hg/lib/mafGene.c
@@ -785,30 +785,33 @@
 
 /* first skip 5' UTR */
 for(; exonStart < lastStart; exonStart++, exonEnd++, frames++)
     {
     int size = *exonEnd - *exonStart;
 
     if (*exonStart + size > pred->cdsStart)
 	break;
     }
 
 for(; exonStart < lastStart; exonStart++, exonEnd++, frames++)
     {
     struct exonInfo *gi;
     int thisStart = *exonStart;
 
+    if (thisStart > pred->cdsEnd)
+	break;
+
     if (thisStart < pred->cdsStart)
 	thisStart = pred->cdsStart;
 
     int thisEnd = *exonEnd;
 
     if (thisEnd > pred->cdsEnd)
 	thisEnd = pred->cdsEnd;
 
     int thisSize = thisEnd - thisStart;
     verbose(3, "in %d %d cds %d %d\n",*exonStart,*exonEnd, thisStart, thisEnd);
 
     AllocVar(gi);
     gi->frame = *frames;
     gi->name = pred->name;
     gi->ali = getAliForRange(database, mafTable, pred->chrom,