7946141cd5729698aa5dcd3ad56815d9a2f3840a
hiram
  Fri Oct 2 13:15:05 2015 -0700
fixup gcc warnings for -Wunused-but-set-variable refs #16121

diff --git src/ameme/fragFind.c src/ameme/fragFind.c
index 98bfddc..8cb12be 100644
--- src/ameme/fragFind.c
+++ src/ameme/fragFind.c
@@ -156,31 +156,30 @@
             bestVal = val;
             bestIx = i;
             }
         }
     }
 return bestIx;
 }
 
 static int fuzzValOne(int *table, int oligoSize, int *rcTable)
 /* Return value of table entry with most number of 
  * matches that are off by no more than one. */
 {
 int tableSize = (1<<(oligoSize+oligoSize));
 int tableIx;
 int bestVal = -0x3ffffff;
-int bestIx;
 
 for (tableIx = 0; tableIx < tableSize; ++tableIx)
     {
     int acc = 0;
     int mask = 0x3;
     int maskedIx;
     int inc = 1;
     int baseIx;
 
     for (baseIx = 0; baseIx<oligoSize; ++baseIx)
         {
         maskedIx = (tableIx&(~mask));
         if (rcTable)
             {
             int mIx = maskedIx;
@@ -193,31 +192,30 @@
             acc += table[rcTable[mIx]];
             }
         acc += table[maskedIx];
         maskedIx += inc;
         acc += table[maskedIx];
         maskedIx += inc;
         acc += table[maskedIx];
         maskedIx += inc;
         acc += table[maskedIx];
         mask <<= 2;
         inc <<= 2;
         }
     if (acc > bestVal)
         {
         bestVal = acc;
-        bestIx = tableIx;
         }
     }
 return tableIx;
 }
 
 static int fuzzValTwo(int *table, int oligoSize, int *rcTable)
 /* Return value of table entry with most number of 
  * matches that are off by no more than one. */
 {
 int tableSize = (1<<(oligoSize+oligoSize));
 int tableIx;
 int bestVal = -0x3ffffff;
 int bestIx = 0;
 
 for (tableIx = 0; tableIx < tableSize; ++tableIx)
@@ -486,39 +484,37 @@
         profile[i][j] = invTotal * counts[i][j];
         }
     }
 }
 
 void fragFind(struct seqList *goodSeq, char *badName, int fragSize, int mismatchesAllowed, 
     boolean considerRc, double profile[16][4])
 /* Do fast finding of patterns that are in FA file "goodName", but not in FA file
  * "badName."  BadName can be null.  Pass in the size of the pattern (fragSize) and
  * the number of mismatches to pattern you're willing to tolerate (mismatchesAllowed).
  * It returns the pattern in profile. */
 {
 int *goodTable, *badTable = NULL;
 int goodCount, badCount = 0;
 int goodIx;
-long startTime;
 DNA unpacked[17];
 
 if (mismatchesAllowed > 3)
     errAbort("Sorry, fragFind can only handle 0-3 mismatches.");
 if (fragSize > 10)
     errAbort("Sorry, fragFind can only handle fragments up to 10 bases.");
 
-startTime = clock1000();
 makeOligoHistogram(NULL, goodSeq, fragSize, &goodTable, &goodCount);
 if (badName)
     makeOligoHistogram(badName, NULL, fragSize, &badTable, &badCount);
 if (badName)
     {
     normalizeTable(goodTable, fragSize);
     normalizeTable(badTable, fragSize);
     diffTables(goodTable, badTable, fragSize);
     goodIx = fuzzVal(badTable, fragSize, mismatchesAllowed, considerRc);
     }
 else
     {
     goodIx = fuzzVal(goodTable, fragSize, mismatchesAllowed, considerRc);
     }
 freez(&goodTable);