ff9313091f342ffe62a124427b5c9d6a516faaea
hiram
  Thu Oct 15 15:03:07 2015 -0700
fixup gcc warnings for -Wunused-but-set-variable refs #16121

diff --git src/hg/hgc/retroClick.c src/hg/hgc/retroClick.c
index 3a93a20..c2c7eba 100644
--- src/hg/hgc/retroClick.c
+++ src/hg/hgc/retroClick.c
@@ -118,53 +118,51 @@
 row = sqlNextRow(sr);
 if (row != NULL)
     {
     mi->gbCurVer = sqlSigned(row[0]);
     mi->sym = cloneString(row[1]);
     mi->desc = cloneString(row[2]);
     }
 sqlFreeResult(&sr);
 }
 
 static struct mappingInfo *mappingInfoNew(struct sqlConnection *conn,
                                           char *tbl, char *mappedId)
 /* load mapping info for a mapped gene */
 {
 struct mappingInfo *mi;
-int preLen;
 char *suffix = containsStringNoCase(tbl,"Info");
 int suffixLen = 4;
 AllocVar(mi);
 if (startsWith("retroAnc", tbl))
     safef(mi->tblPre, sizeof(mi->tblPre), "retroAnc");
 else if (startsWith("retroOld", tbl))
     safef(mi->tblPre, sizeof(mi->tblPre), "retroOld");
 else if (startsWith("retro", tbl))
     safef(mi->tblPre, sizeof(mi->tblPre), "retro");
 else
     {
     safef(mi->tblPre, sizeof(mi->tblPre), "ucsc");
     suffix = containsStringNoCase(tbl,"Ali");
     suffixLen = 3;
     }
 if (suffix != NULL)
     {
     suffix +=suffixLen;
     safef(mi->suffix,ID_BUFSZ,"%s",suffix);
     }
 
-preLen = strlen(mi->tblPre);
 if (startsWith("retroAugust", tbl))
     safef(mi->geneSet, sizeof(mi->geneSet), "August");
 else if (startsWith("retro", tbl))
     safef(mi->geneSet, sizeof(mi->geneSet), "Mrna");
 else
     safef(mi->geneSet, sizeof(mi->geneSet), "Retro");
 if (suffix != NULL && strlen(suffix) > 0)
     mi->pg = sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad, sqlQueryMust|sqlQuerySingle,
                       "select * from %s%sInfo%s where name='%s'", mi->tblPre, mi->geneSet, suffix,
                        mappedId);
 else
     {
     mi->pg = sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad, sqlQueryMust|sqlQuerySingle,
                       "select * from %s%sInfo where name='%s'", mi->tblPre, mi->geneSet,
                        mappedId);
@@ -298,80 +296,77 @@
     float coverage = 0;
     if (psl->strand[0] == '-')
         reverseIntRange(&qs, &qe, psl->qSize);
     overlap = positiveRangeIntersection(start, end, qs, qe);
     coverage = (float)overlap/(float)(qe-qe);
     total += overlap;
     if (overlap > 25 || coverage > 0.4)
          blocks++;
     }
 *numBlocks = blocks;
 return total;
 }
 
 void printBlocks (struct psl *psl, int maxBlockGap, struct psl *nestedPsl)
 {
-int i, qsStart = 0;
+int i;
 int exonsCovered = 0;
 int totalBases = 0;
 int totalExons = 0;
 int intronsPresent = 0;
 int intronsPresentBases = 0;
 int intronsSpliced = 0;
 for (i = 0 ; i < psl->blockCount ; i++)
     {
     int qs = psl->qStarts[i];
     int qe = psl->qStarts[i] + psl->blockSizes[i];
     int te = psl->tStarts[i] + psl->blockSizes[i];
     int tdiff = 0;
     int qdiff = 0;
     int cumTdiff = 0;
     int oqs, oqe;
     int tsNext = 999999;
     int qsNext = 0;
     float coverage = 0;
     int bases = 0;
-    int oldte = te;
     int gapRatio = 0;
     if (i < psl->blockCount -1)
         {
         tsNext = psl->tStarts[i+1];
         qsNext = psl->qStarts[i+1];
         tdiff = tsNext - te;
         qdiff = qsNext - qe;
         }
     else
         tdiff = 9999999;
     cumTdiff = tdiff;
-    qsStart = qs;
 /* combine blocks that are close together */
     while (tdiff < maxBlockGap && i< (psl->blockCount)-1)
         {
         i++;
         te = psl->tStarts[i] + psl->blockSizes[i];
         qe = psl->qStarts[i] + psl->blockSizes[i];
         if (i < psl->blockCount -1)
             {
             tsNext = psl->tStarts[i+1];
             qsNext = psl->qStarts[i+1];
             tdiff = tsNext - te;
             qdiff = qsNext - qe;
             }
         else
             tdiff = 9999999;
         cumTdiff += tdiff;
-        oldte = te;
         }
     oqs = qs; oqe = qe;
     if (psl->strand[0] == '-')
         reverseIntRange(&oqs, &oqe, psl->qSize);
     gapRatio = qdiff*100/tdiff;
     printf("%d-%d:%d",oqs,oqe,gapRatio); 
     if (gapRatio < 30 && tdiff > 30 && 
             i < (psl->blockCount)-1)
         {
         int bases = (tdiff-qdiff > 0) ? tdiff - qdiff : 0;
         intronsPresent++;
         intronsPresentBases += bases;
         }
     if (nestedPsl != NULL)
         {