39d5a3814a81cfe2431d161a1e044ec44e2f6504
hiram
  Wed Nov 25 11:16:51 2015 -0800
fixup gcc warnings for -Wunused-but-set-variable refs #16121

diff --git src/hg/sim4big/sim4big.c src/hg/sim4big/sim4big.c
index 4208bb3..eb093e1 100644
--- src/hg/sim4big/sim4big.c
+++ src/hg/sim4big/sim4big.c
@@ -145,31 +145,30 @@
     for (block = blockList; block != NULL; block = block->next)
 	fprintf(f, "%d,", block->tStart);
     fprintf(f, "\n");
     }
 }
 
 void parseIntoBed(char *sim4out, 
 	char *qName, int qSize, char *tName, int tSize, FILE *f)
 /* Parse a sim4 output file and put it into bed file. */
 {
 struct lineFile *lf = lineFileOpen(sim4out, TRUE);
 char *line, *row[3], *parts[3];
 int partCount;
 boolean isRc = FALSE;
 struct block *blockList = NULL, *block;
-int bases;
 
 /* Read header and remember if complemented. */
 if (!lineFileNext(lf, &line, NULL))
    errAbort("%s is empty", lf->fileName);
 if (!lineFileNext(lf, &line, NULL) || !startsWith("seq1", line))
    errAbort("%s doesn't seem to be a sim4 output file", lf->fileName);
 lineFileNext(lf, &line, NULL);
 lineFileNext(lf, &line, NULL);
 lineFileNext(lf, &line, NULL);
 if (startsWith("(complement)", line))
    isRc = TRUE;
 else
    lineFileReuse(lf);
 
 /* Parse rest of file into blockList. */
@@ -177,31 +176,30 @@
     {
     AllocVar(block);
     partCount = chopString(row[0], "-", parts, ArraySize(parts));
     if (partCount != 2 || !isdigit(parts[0][0]) || !isdigit(parts[1][0]))
         sim4BadLine(lf);
     block->qStart = atoi(parts[0]) - 1;
     block->qEnd = atoi(parts[1]);
     partCount = chopString(row[1], "(-)", parts, ArraySize(parts));
     if (partCount != 2 || !isdigit(parts[0][0]) || !isdigit(parts[1][0]))
         sim4BadLine(lf);
     block->tStart = atoi(parts[0]) - 1;
     block->tEnd = atoi(parts[1]);
     if (!isdigit(row[2][0]))
         sim4BadLine(lf);
     block->percentId = atoi(row[2]);
-    bases = block->qStart - block->qEnd;
     slAddHead(&blockList, block);
     }
 lineFileClose(&lf);
 slReverse(&blockList);
 outputBlocks(blockList, f, isRc, qName, qSize, tName, tSize, FALSE);
 slFreeList(&blockList);
 }
 
 void parseIntoPsl(char *lavFile, 
 	char *qName, int qSize, char *tName, int tSize, FILE *f)
 /* Parse a sim4 lav file and put it into something .psl like. */
 {
 struct lineFile *lf = lineFileOpen(lavFile, TRUE);
 char *line, *words[10];
 boolean gotAli = FALSE;