6da21892974e02baf3cc797a443ca1a97ba80a78
hartera
  Wed Jul 25 15:53:12 2012 -0700
Changed variable name to one that better describes its function.
diff --git src/hg/lib/mafGene.c src/hg/lib/mafGene.c
index 4b5da13..670b3d6 100644
--- src/hg/lib/mafGene.c
+++ src/hg/lib/mafGene.c
@@ -759,92 +759,92 @@
     giNext = list->next;
 
     mafAliFreeList(&list->ali);
     }
 }
  
 static struct exonInfo *buildGIList(char *database, struct genePred *pred, 
     char *mafTable, unsigned options)
 {
 struct exonInfo *giList = NULL;
 unsigned *exonStart = pred->exonStarts;
 unsigned *lastStart = &exonStart[pred->exonCount];
 unsigned *exonEnd = pred->exonEnds;
 int *frames = pred->exonFrames;
 
-boolean utr = options & MAFGENE_UTR;
+boolean includeUtr = options & MAFGENE_INCLUDEUTR;
 
 if (frames == NULL)
     {
     genePredAddExonFrames(pred);
     frames = pred->exonFrames;
     }
 
 assert(frames != NULL);
 
 int start = 0;
 
 
 /* first skip 5' UTR if the includeUtr option is not set */
-if (!utr) 
+if (!includeUtr) 
     {
     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;
     int thisEnd = *exonEnd;
     
-    if (!utr) 
+    if (!includeUtr) 
         {
         if (thisStart > pred->cdsEnd)
 	    break;
 
         if (thisStart < pred->cdsStart)
 	    thisStart = pred->cdsStart;
 
 
         if (thisEnd > pred->cdsEnd)
 	    thisEnd = pred->cdsEnd;
         
 	}
     int thisSize = thisEnd - thisStart;
-    if (!utr)
+    if (!includeUtr)
         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, 
 	thisStart, thisEnd);
     gi->chromStart = thisStart;
     gi->chromEnd = thisEnd;
     gi->exonStart = start;
     gi->exonSize = thisSize;
     verbose(3, "exon size %d\n", thisSize);
     gi->strand = pred->strand[0];
     start += gi->exonSize;
     slAddHead(&giList, gi);
  
-    if (!utr) 
+    if (!includeUtr) 
         {
         if (thisEnd == pred->cdsEnd)
 	    break;
         }
     }
 slReverse(&giList);
 
 return giList;
 }
 
 void mafGeneOutPred(FILE *f, struct genePred *pred, char *dbName, 
     char *mafTable,  struct slName *speciesNameList, unsigned options,
     int numCols) 
 {
 boolean inExons = options & MAFGENE_EXONS;