removed a few unused variables

These variables have been assigned but never actually used. Reported by
gcc-4.7. Lower version cannot give such warnings.

QSufSort.c

@@ -59,12 +59,9 @@ void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsin
 	qsint_t i, j;
 	qsint_t s, negatedSortedGroupLength;
 	qsint_t numSymbolAggregated;
-	qsint_t maxNumInputSymbol;
 	qsint_t numSortedPos = 1;
 	qsint_t newAlphabetSize;
 
-	maxNumInputSymbol = largestInputSymbol - smallestInputSymbol + 1;
-
 	if (!skipTransform) {
 		/* bucketing possible*/
 		newAlphabetSize = QSufSortTransform(V, I, numChar, largestInputSymbol, smallestInputSymbol, 

bwamem.c

@@ -418,7 +418,7 @@ static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
 void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *av)
 { // FIXME: in general, we SHOULD check funny seed patterns such as contained seeds. When that happens, we should use a SW or extend more seeds
 	int i, k;
-	int64_t rlen, rmax[2], tmp, max = 0, max_i = 0;
+	int64_t rlen, rmax[2], tmp, max = 0;
 	const mem_seed_t *s;
 	uint8_t *rseq = 0;
 
@@ -432,7 +432,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 		e = t->rbeg + t->len + ((l_query - t->qbeg - t->len) + cal_max_gap(opt, l_query - t->qbeg - t->len));
 		rmax[0] = rmax[0] < b? rmax[0] : b;
 		rmax[1] = rmax[1] > e? rmax[1] : e;
-		if (t->len > max) max = t->len, max_i = i;
+		if (t->len > max) max = t->len;
 	}
 	// retrieve the reference sequence
 	rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen);
@@ -523,7 +523,7 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
 void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, const bwahit_t *p_, int is_hard, const bwahit_t *m)
 {
 #define is_mapped(x) ((x)->rb >= 0 && (x)->rb < (x)->re && (x)->re <= bns->l_pac<<1)
-	int score, n_cigar, is_rev = 0, nn, rid, mid, copy_mate = 0;
+	int score, n_cigar, is_rev = 0, rid, mid, copy_mate = 0;
 	uint32_t *cigar = 0;
 	int64_t pos;
 	bwahit_t ptmp, *p = &ptmp;
@@ -548,7 +548,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
 			p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)
 		} else n_cigar = 0, cigar = 0;
 		pos = bns_depos(bns, p->rb < bns->l_pac? p->rb : p->re - 1, &is_rev);
-		nn = bns_cnt_ambi(bns, pos, p->re - p->rb, &rid);
+		bns_cnt_ambi(bns, pos, p->re - p->rb, &rid);
 		kputw(p->flag, str); kputc('\t', str);
 		kputs(bns->anns[rid].name, str); kputc('\t', str); kputuw(pos - bns->anns[rid].offset + 1, str); kputc('\t', str);
 		kputw(p->qual, str); kputc('\t', str);
@@ -569,7 +569,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
 	}
 	if (m && is_mapped(m)) { // then print mate pos and isize
 		pos = bns_depos(bns, m->rb < bns->l_pac? m->rb : m->re - 1, &is_rev);
-		nn = bns_cnt_ambi(bns, pos, m->re - m->rb, &mid);
+		bns_cnt_ambi(bns, pos, m->re - m->rb, &mid);
 		kputc('\t', str);
 		if (mid == rid) kputc('=', str);
 		else kputs(bns->anns[mid].name, str);

bwase.c

@@ -71,8 +71,8 @@ void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_ma
 				}
 				rest -= q->l - q->k + 1;
 			} else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here. 
-				int j, i, k;
-				for (j = rest, i = q->l - q->k + 1, k = 0; j > 0; --j) {
+				int j, i;
+				for (j = rest, i = q->l - q->k + 1; j > 0; --j) {
 					double p = 1.0, x = drand48();
 					while (x < p) p -= p * j / (i--);
 					s->multi[z].pos = q->l - i;
@@ -412,11 +412,11 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 
 		// print mate coordinate
 		if (mate && mate->type != BWA_TYPE_NO_MATCH) {
-			int m_seqid, m_is_N;
+			int m_seqid;
 			long long isize;
 			am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
 			// redundant calculation here, but should not matter too much
-			m_is_N = bns_cnt_ambi(bns, mate->pos, mate->len, &m_seqid);
+			bns_cnt_ambi(bns, mate->pos, mate->len, &m_seqid);
 			err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
 			isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
 			if (p->type == BWA_TYPE_NO_MATCH) isize = 0;

bwtsw2_aux.c

@@ -186,14 +186,14 @@ static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8
 		bsw2aux_t *q = b->aux + i;
 		uint8_t *query;
 		bwtint_t k;
-		int score, path_len, beg, end;
+		int path_len, beg, end;
 		if (p->l) continue;
 		beg = (p->flag & 0x10)? lq - p->end : p->beg;
 		end = (p->flag & 0x10)? lq - p->beg : p->end;
 		query = seq[(p->flag & 0x10)? 1 : 0] + beg;
 		for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
 			target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
-		score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
+		aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
 		q->cigar = aln_path2cigar32(path, path_len, &q->n_cigar);
 #if 0
 		if (name && score != p->G) { // debugging only

stdaln.c

@@ -542,13 +542,12 @@ int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2,
 	int start, end, max_score;
 	int thres, *suba, *ss;
 
-	int gap_open, gap_ext, b;
+	int gap_open, gap_ext;
 	int *score_matrix, N_MATRIX_ROW;
 
 	/* initialize some align-related parameters. just for compatibility */
 	gap_open = ap->gap_open;
 	gap_ext = ap->gap_ext;
-	b = ap->band_width;
 	score_matrix = ap->matrix;
 	N_MATRIX_ROW = ap->row;
 	thres = _thres > 0? _thres : -_thres;
@@ -862,7 +861,7 @@ uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
 int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
 					path_t *path, int *path_len, int G0, uint8_t *_mem)
 {
-	int q, r, qr, tmp_len;
+	int q, r, qr;
 	int32_t **s_array, *score_array;
 	int is_overflow, of_base;
 	uint32_t *eh;
@@ -889,7 +888,6 @@ int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2
 		s_array[i] = (int32_t*)_p, _p += 4 * len1;
 	/* initialization */
 	aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
-	tmp_len = len1 + 1;
 	start = 1; end = 2;
 	end_i = end_j = 0;
 	score = 0;