ae805eabd626edf7912d09d380b086ec7ebbb104
hiram
  Fri Oct 2 13:13:35 2015 -0700
fixup gcc warnings for -Wunused-but-set-variable refs #16121

diff --git src/ameme/ameme.c src/ameme/ameme.c
index 25faf3a..ad9626a 100644
--- src/ameme/ameme.c
+++ src/ameme/ameme.c
@@ -1445,31 +1445,31 @@
     }
 else if (retProfile != NULL)
 /* Generate next generation profile if that's what they want. */
     {
     int profSize = prof->columnCount;
     struct profileColumn *col;
     struct profileColumn *column, *rcColumn = NULL;
     struct profile *newProf = blankProfile(profSize);
     struct profile *rcNewProf = NULL;
     struct dnaSeq *seq;
     DNA *dna;
     int colIx;
     double minSd = 1.0;
     double sd;
     int shiftLeftEnd = 0, shiftRightEnd = 0;
-    int rcShiftLeftEnd = 0, rcShiftRightEnd = 0;
+    int rcShiftLeftEnd = 0;
     int newProfScore;
     struct position *pos;
     boolean doResize = (constrainer < 900.0);
     double **tempColProbs = getTempColProbs(profSize);
 
     /* Go through hits and use them to generate next generation
      * of profile. */
     for (pos = posList; pos != NULL; pos = pos->next)
         {
         onePos = pos->pos;
         seqEl = pos->seqEl;
         weight = pos->weight;
         seq = seqEl->seq;
         dna = seq->dna + onePos;
         if (pos->isRc)
@@ -1533,31 +1533,30 @@
             int newCount = newProf->columnCount-1;
             column = newProf->columns->next;
             if (rcNewProf)
                 rcColumn = rcNewProf->columns;
             newProfScore = scoreAtPositions(column, rcColumn, newCount,
                 posList, 1, 0, seqCount);
             if (newProfScore > profScore)
                 {
                 shiftLeftEnd = 1;
                 profScore = newProfScore;
                 removeFirstColumn(newProf);
                 newProf->locale.mean += 1.0;
                 if (rcNewProf)
                     {
                     removeLastColumn(rcNewProf);
-                    rcShiftRightEnd = -1;
                     }
                 }
             }
 
         /* See if profile improves by subtracting column to right */
         if (newProf->columnCount > 1)
             {
             int newCount = newProf->columnCount-1;
             column = newProf->columns;
             if (rcNewProf)
                 rcColumn = rcNewProf->columns->next;
             newProfScore = scoreAtPositions(column, rcColumn, newCount,
                 posList, shiftLeftEnd, 1, seqCount);
             if (newProfScore > profScore)
                 {
@@ -1585,34 +1584,30 @@
                 column = newProf->columns;
                 if (rcNewProf)
                     {
                     struct profileColumn *rcCol = rcColumnCopy(col);
                     slAddTail(&rcNewProf->columns, rcCol);
                     rcNewProf->columnCount = newCount;
                     rcColumn = rcNewProf->columns;
                     }
                 newProfScore = scoreAtPositions(column, rcColumn, newCount,
                     posList, -1, rcShiftLeftEnd, seqCount);
                 if (newProfScore > profScore + expandConstrainFactor)
                     {
                     newProf->locale.mean -= 1.0;
                     shiftLeftEnd = -1;
                     profScore = newProfScore;
-                    if (rcNewProf)
-                        {
-                        rcShiftRightEnd = 1;
-                        }
                     }
                 else
                     {
                     removeFirstColumn(newProf);
                     if (rcNewProf)
                         removeLastColumn(rcNewProf);
                     }
                 }
             }
 
         /* See if profile improves by adding a column to the right */
         if (!shiftRightEnd)
             {
             col = columnAtPositions(posList, profSize, profSize);
             if (col != NULL)