b3aedfa46a48ead09c1cdedf34b07b281ea1ae18
hiram
  Fri Oct 2 10:41:11 2015 -0700
fixup gcc warnings for -Wunused-but-set-variable refs #16121

diff --git src/jkOwnLib/xensmall.c src/jkOwnLib/xensmall.c
index 595b772..3c6559d 100644
--- src/jkOwnLib/xensmall.c
+++ src/jkOwnLib/xensmall.c
@@ -208,58 +208,57 @@
 //hiFiMatchBonus = scaledLogOfFraction(0.9, 0.25);
 //hiFiMismatchCost = scaledLogOfFraction(0.1, 0.75);
 }
 
 
 int xenAlignSmall(DNA *query, int querySize, DNA *target, int targetSize, FILE *f,
     boolean printExtraAtEnds)
 /* Use dynamic programming to do small scale (querySize * targetSize < 10,000,000)
  * alignment of DNA. */
 {
 struct phmmMatrix *a;
 struct phmmState *hf, *lf, *iq, *it, *c1, *c2, *c3;
 int qIx, tIx, sIx;  /* Query, target, and state indices */
 int rowOffset, newCellOffset;
 struct phmmAliPair *pairList;
-int matchOff, qSlipOff, tSlipOff;
 int bestScore = -0x4fffffff;
 struct phmmMommy *bestCell = NULL;
 int c1c2PairScore, c3PairScore, loFiPairScore, hiFiPairScore;
 int matchTableOffset;
 double gcRatio;
 
 /* Check that it's not too big. */
 if ((double)targetSize * querySize > 1.1E7)
     errAbort("Can't align %d x %d, too big\n", querySize, targetSize);
 
 /* Set up graph edge costs/benefits */
 gcRatio = calcGcRatio(query, querySize, target, targetSize);
 calcCostBenefit(gcRatio);
 
 /* Initialize 7 state matrix. */
 a = phmmMatrixNew(7, query, querySize, target, targetSize);
 hf = phmmNameState(a, hiFiIx, "highFi", 'H');
 lf = phmmNameState(a, loFiIx, "lowFi", 'L');
 iq = phmmNameState(a, qSlipIx, "qSlip", 'Q');
 it = phmmNameState(a, tSlipIx, "tSlip", 'T');
 c1 = phmmNameState(a, c1Ix, "frame1", '1');
 c2 = phmmNameState(a, c2Ix, "frame2", '2');
 c3 = phmmNameState(a, c3Ix, "frame3", '3');
 
-qSlipOff = -a->qDim;
-tSlipOff = -1;
-matchOff = qSlipOff + tSlipOff;
+// int qSlipOff = -a->qDim;  unnecessary
+// int tSlipOff = -1;  unnecessary
+// int matchOff = qSlipOff + tSlipOff;  unnecessary
 
 for (tIx = 1; tIx < a->tDim; tIx += 1)
     {
     UBYTE mommy = 0;
     int score, tempScore;
 
 /* Macros to make me less mixed up when accessing scores from row arrays.*/
 #define matchScore lastScores[qIx-1]
 #define qSlipScore lastScores[qIx]
 #define tSlipScore scores[qIx-1]
 #define newScore scores[qIx]
 
 /* Start up state block (with all ways to enter state) */
 #define startState(state) \
    score = 0;