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r792: fixed -Wextra warnings and resolved #184

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This commit is contained in:
Heng Li
2018-06-19 15:26:58 -04:00
parent 408e098859
commit 7e6e8ca73f
15 changed files with 67 additions and 58 deletions
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align.c
+12 -11
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@@ -91,7 +91,8 @@ static int mm_test_zdrop(void *km, const mm_mapopt_t *opt, const uint8_t *qseq,
static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, int *qshift, int *tshift)
{
mm_extra_t *p = r->p;
int32_t k, toff = 0, qoff = 0, to_shrink = 0;
int32_t toff = 0, qoff = 0, to_shrink = 0;
uint32_t k;
*qshift = *tshift = 0;
if (p->n_cigar <= 1) return;
for (k = 0; k < p->n_cigar; ++k) { // indel left alignment
@@ -148,8 +149,8 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e)
{
uint32_t k, l, toff = 0, qoff = 0;
int32_t s = 0, max = 0, qshift, tshift;
uint32_t k, l;
int32_t s = 0, max = 0, qshift, tshift, toff = 0, qoff = 0;
mm_extra_t *p = r->p;
if (p == 0) return;
mm_fix_cigar(r, qseq, tseq, &qshift, &tshift);
@@ -407,7 +408,7 @@ static void mm_filter_bad_seeds_alt(void *km, int as1, int cnt1, mm128_t *a, int
int re1 = (int32_t)a[as1 + i].x;
int qe1 = (int32_t)a[as1 + i].y;
gap1 = gap1 > 0? gap1 : -gap1;
for (l = k + 1; l < n && a[as1 + K[l]].y - a[as1 + i].y <= max_ext; ++l) {
for (l = k + 1; l < n && a[as1 + K[l]].y <= a[as1 + i].y + max_ext; ++l) {
int j = K[l];
int gap2 = ((int32_t)a[as1 + j].y - a[as1 + j - 1].y) - ((int32_t)a[as1 + j].x - a[as1 + j - 1].x);
int q_span_pre = a[as1 + j - 1].y >> 32 & 0xff;
@@ -467,7 +468,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
}
}
static void mm_max_stretch(const mm_mapopt_t *opt, const mm_reg1_t *r, const mm128_t *a, int32_t *as, int32_t *cnt)
static void mm_max_stretch(const mm_reg1_t *r, const mm128_t *a, int32_t *as, int32_t *cnt)
{
int32_t i, score, max_score, len, max_i, max_len;
@@ -505,7 +506,7 @@ static int mm_seed_ext_score(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
qe = (uint32_t)a->y + 1, qs = qe - q_span;
rs = rs - ext_len > 0? rs - ext_len : 0;
qs = qs - ext_len > 0? qs - ext_len : 0;
re = re + ext_len < mi->seq[rid].len? re + ext_len : mi->seq[rid].len;
re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len;
qe = qe + ext_len < qlen? qe + ext_len : qlen;
tseq = (uint8_t*)kmalloc(km, re - rs);
mm_idx_getseq(mi, rid, rs, re, tseq);
@@ -555,7 +556,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
bw = (int)(opt->bw * 1.5 + 1.);
if (is_sr && !(mi->flag & MM_I_HPC)) {
mm_max_stretch(opt, r, a, &as1, &cnt1);
mm_max_stretch(r, a, &as1, &cnt1);
rs = (int32_t)a[as1].x + 1 - (int32_t)(a[as1].y>>32&0xff);
qs = (int32_t)a[as1].y + 1 - (int32_t)(a[as1].y>>32&0xff);
re = (int32_t)a[as1+cnt1-1].x + 1;
@@ -591,7 +592,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
rs0 = rs - l > 0? rs - l : 0;
l = qlen - qe;
l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
re0 = re + l < mi->seq[rid].len? re + l : mi->seq[rid].len;
re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len;
} else {
// compute rs0 and qs0
rs0 = (int32_t)a[r->as].x + 1 - (int32_t)(a[r->as].y>>32&0xff);
@@ -635,13 +636,13 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
}
}
}
if (qe < qlen && re < mi->seq[rid].len) {
if (qe < qlen && re < (int32_t)mi->seq[rid].len) {
l = qlen - qe < opt->max_gap? qlen - qe : opt->max_gap;
qe1 = qe1 < qe + l? qe1 : qe + l;
qe0 = qe0 > qe1? qe0 : qe1; // at least include qe0
l += l * opt->a > opt->q? (l * opt->a - opt->q) / opt->e : 0;
l = l < opt->max_gap? l : opt->max_gap;
l = l < mi->seq[rid].len - re? l : mi->seq[rid].len - re;
l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re;
re1 = re1 < re + l? re1 : re + l;
re0 = re0 > re1? re0 : re1;
} else re0 = re, qe0 = qe;
@@ -875,7 +876,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
*n_regs_ = n_regs;
kfree(km, qseq0[0]);
kfree(km, ez.cigar);
mm_filter_regs(km, opt, qlen, n_regs_, regs);
mm_filter_regs(opt, qlen, n_regs_, regs);
mm_hit_sort_by_dp(km, n_regs_, regs);
return regs;
}