0886e7b5c34b188b9030e65199c5368592c486c5
markd
  Tue Nov 24 20:28:35 2015 -0800
fixed unused variable warnings

diff --git src/hg/hgc/retroClick.c src/hg/hgc/retroClick.c
index c2c7eba..2f83a78 100644
--- src/hg/hgc/retroClick.c
+++ src/hg/hgc/retroClick.c
@@ -496,77 +496,77 @@
 int i;
 int count = 0;
 for (i=0; i<(gp->exonCount); i++)
     {
     if ( (gp->cdsStart <= gp->exonEnds[i]) &&  
          (gp->cdsEnd >= gp->exonStarts[i]) )
          count++;
     }
 return count;
 
 }
 static void displayMappingInfo(struct sqlConnection *conn, struct mappingInfo *mi)
 /* display information from a transMap table */
 {
 struct ucscRetroInfo *pg = mi->pg;
-double  wt[12];     /* weights on score function*/
 char query[512];
 char *name;
 char alignTbl[128];
 char scoreSql[128];
+#ifdef score
+double  wt[12];     /* weights on score function*/
 struct psl *psl;
 float coverFactor = 0;
 float maxOverlap = 0;
+#endif
 if (mi->suffix == NULL)
     {
     safef(alignTbl, sizeof(alignTbl), "%s%sAli", mi->tblPre, mi->geneSet);
     sqlSafef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo", mi->tblPre, mi->geneSet);
     }
 else
     {
     safef(alignTbl, sizeof(alignTbl), "%s%sAli%s", mi->tblPre, mi->geneSet, mi->suffix);
     sqlSafef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo%s", mi->tblPre, mi->geneSet, mi->suffix);
     }
 printf("<TABLE class=\"transMap\">\n");
 printf("<H3>Retrogene Statistics:</H3>\n");
 printf("<THEAD>\n");
 printf("<TR><TH>Feature<TH>Value </TR>\n");
 printf("</THEAD><TBODY>\n");
 if (sameString(pg->type, "singleExon"))
     printf("<TR><TH>Type of Parent<TD>%s</tr>\n",pg->type);
 else 
     printf("<TR><TH>Expression of Retrogene<TD>%s</TR>\n",pg->type);
 printf("<TR><TH>Score <TD>%d (range from 0 - %d)</TR>\n",  
         pg->score,
         sqlQuickNum(conn, scoreSql) );
 printf("<TR><TH>Parent Gene Alignment Coverage (Bases&nbsp;Matching Parent) <TD>%d %% &nbsp;(%d bp) </TR>\n", pg->coverage, pg->matches);
 printf("<TR><TH>Introns Processed Out <TD>%d out of %d (%d exons covered)\n", pg->processedIntrons, (pg->parentSpliceCount/2), pg->exonCover);
 printf("<TR><TH>Possible Introns or Gaps in Retrogene<TD>%d,%d\n", pg->intronCount, pg->alignGapCount);
 printf("<TR><TH>Conserved Splice Sites<TD>%d</TR>\n",  pg->conservedSpliceSites);
 printf("<TR><TH>Parent Splice Sites<TD>%d</TR>\n",  pg->parentSpliceCount);
+#ifdef score
 psl = getAlignments(conn, alignTbl, mi->pg->name);
 if (psl != NULL)
     {
     maxOverlap = (float)pg->maxOverlap/(float)(psl->match+psl->misMatch+psl->repMatch)  ;
     coverFactor = ((float)(psl->qSize-psl->qEnd)/(float)psl->qSize);
     }
-else 
-    {
-    maxOverlap = 0;
-    }
 wt[0] = 0; wt[1] = 0.85; wt[2] = 0.2; wt[3] = 0.3; wt[4] = 0.8; 
 wt[5] = 1; wt[6] = 1  ; wt[7] = 0.5; wt[8] = 0.5; wt[9] = 1; wt[10] = 1;
+#endif
 #ifdef debug
 char table[512];
 struct psl *pslList = getParentAligns(conn, mi, &table);
 if (psl != NULL)
     {
     printf("<TR><TH>Blocks in retro:gap%%/intronsSpliced <TD>\n");
     printBlocks(psl, MAXBLOCKGAP, pslList);
     printf("</td></TR>\n");  
     }
 if (pslList != NULL)
     {
     printf("<TR><TH>Exons in parent:gap%% <TD>\n");
     printBlocks(pslList, MAXBLOCKGAP, NULL);
     printf("</td></TR>\n");  
     pslFreeList(&pslList);