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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.
This commit is contained in:
Heng Li 2013-02-23 13:26:50 -05:00
parent 6230f86799
commit 904c3205c0
5 changed files with 13 additions and 18 deletions
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3
QSufSort.c
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@ -59,12 +59,9 @@ void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsin
qsint_t i, j; qsint_t i, j;
qsint_t s, negatedSortedGroupLength; qsint_t s, negatedSortedGroupLength;
qsint_t numSymbolAggregated; qsint_t numSymbolAggregated;
qsint_t maxNumInputSymbol;
qsint_t numSortedPos = 1; qsint_t numSortedPos = 1;
qsint_t newAlphabetSize; qsint_t newAlphabetSize;
maxNumInputSymbol = largestInputSymbol - smallestInputSymbol + 1;
if (!skipTransform) { if (!skipTransform) {
/* bucketing possible*/ /* bucketing possible*/
newAlphabetSize = QSufSortTransform(V, I, numChar, largestInputSymbol, smallestInputSymbol, newAlphabetSize = QSufSortTransform(V, I, numChar, largestInputSymbol, smallestInputSymbol,

10
bwamem.c
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@ -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) 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 { // 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; 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; const mem_seed_t *s;
uint8_t *rseq = 0; 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)); 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[0] = rmax[0] < b? rmax[0] : b;
rmax[1] = rmax[1] > e? rmax[1] : e; 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 // retrieve the reference sequence
rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen); rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen);
@ -523,7 +523,7 @@ ret_gen_cigar:
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) 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) #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; uint32_t *cigar = 0;
int64_t pos; int64_t pos;
bwahit_t ptmp, *p = &ptmp; 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) p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)
} else n_cigar = 0, cigar = 0; } else n_cigar = 0, cigar = 0;
pos = bns_depos(bns, p->rb < bns->l_pac? p->rb : p->re - 1, &is_rev); 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); 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); 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); 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 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); 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); kputc('\t', str);
if (mid == rid) kputc('=', str); if (mid == rid) kputc('=', str);
else kputs(bns->anns[mid].name, str); else kputs(bns->anns[mid].name, str);

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

4
bwtsw2_aux.c
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@ -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; bsw2aux_t *q = b->aux + i;
uint8_t *query; uint8_t *query;
bwtint_t k; bwtint_t k;
int score, path_len, beg, end; int path_len, beg, end;
if (p->l) continue; if (p->l) continue;
beg = (p->flag & 0x10)? lq - p->end : p->beg; beg = (p->flag & 0x10)? lq - p->end : p->beg;
end = (p->flag & 0x10)? lq - p->beg : p->end; end = (p->flag & 0x10)? lq - p->beg : p->end;
query = seq[(p->flag & 0x10)? 1 : 0] + beg; 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 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; 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); q->cigar = aln_path2cigar32(path, path_len, &q->n_cigar);
#if 0 #if 0
if (name && score != p->G) { // debugging only if (name && score != p->G) { // debugging only

6
stdaln.c
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@ -542,13 +542,12 @@ int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2,
int start, end, max_score; int start, end, max_score;
int thres, *suba, *ss; int thres, *suba, *ss;
int gap_open, gap_ext, b; int gap_open, gap_ext;
int *score_matrix, N_MATRIX_ROW; int *score_matrix, N_MATRIX_ROW;
/* initialize some align-related parameters. just for compatibility */ /* initialize some align-related parameters. just for compatibility */
gap_open = ap->gap_open; gap_open = ap->gap_open;
gap_ext = ap->gap_ext; gap_ext = ap->gap_ext;
b = ap->band_width;
score_matrix = ap->matrix; score_matrix = ap->matrix;
N_MATRIX_ROW = ap->row; N_MATRIX_ROW = ap->row;
thres = _thres > 0? _thres : -_thres; 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, 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) 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; int32_t **s_array, *score_array;
int is_overflow, of_base; int is_overflow, of_base;
uint32_t *eh; 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; s_array[i] = (int32_t*)_p, _p += 4 * len1;
/* initialization */ /* initialization */
aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array); aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
tmp_len = len1 + 1;
start = 1; end = 2; start = 1; end = 2;
end_i = end_j = 0; end_i = end_j = 0;
score = 0; score = 0;