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clean bill from valgrind

This commit is contained in:
Heng Li 2017-05-04 12:44:49 +08:00
parent 7b53f7aa84
commit 06adabd0dc
2 changed files with 22 additions and 10 deletions
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2
main.c
View File

@ -22,7 +22,7 @@ void liftrlimit()
int main(int argc, char *argv[])
{
mm_mapopt_t opt;
int i, c, k = 15, w = -1, b = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx = 0, is_hpc = 0;
int i, c, k = 17, w = -1, b = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx = 0, is_hpc = 0;
int mini_batch_size = 100000000;
uint64_t batch_size = 4000000000ULL;
bseq_file_t *fp = 0;

30
map.c
View File

@ -9,6 +9,7 @@
void mm_mapopt_init(mm_mapopt_t *opt)
{
memset(opt, 0, sizeof(mm_mapopt_t));
opt->n_frag_mini = 100;
opt->max_occ_frac = 1e-5f;
opt->mid_occ_frac = 2e-4f;
@ -113,7 +114,7 @@ int mm_pair_thin_core(mm_tbuf_t *b, uint64_t x, int radius, int rel, int st0, in
}
}
return en;
} else return z[st] < x? st + 1 : en;
} else return st < n && z[st] < x? st + 1 : en;
}
void mm_pair_thin(mm_tbuf_t *b, int radius, mm_match_t *m1, mm_match_t *m2)
@ -167,7 +168,9 @@ int mm_liss(int d, int min_L, void *km, int n, mm128_t *a, int *b)
if (L >= min_L) { // save the chain if long enough
int k;
for (k = L - 1; k >= 0; --k)
a[o + k] = a[j], j = P[j];
M[k] = j, j = P[j];
for (k = 0; k < L; ++k)
a[o + k] = a[M[k]];
o += L;
b[m++] = L;
}
@ -233,18 +236,19 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
if (m[i].n < opt->mid_occ) n_a += m[i].n;
// fill the _a_ array
a = kmalloc(b->km_fixed, n_a * sizeof(mm128_t));
a = (mm128_t*)kmalloc(b->km_fixed, n_a * sizeof(mm128_t));
for (i = j = 0; i < n; ++i) {
mm_match_t *q = &m[i];
const uint64_t *r = q->x.cr;
int k;
if (q->n >= opt->mid_occ) continue;
for (k = 0; k < q->n; ++k) {
const char *tname = mi->seq[r[k]>>32].name;
int32_t rpos = (uint32_t)r[k] >> 1;
mm128_t *p;
if (qname && (opt->flag&MM_F_NO_SELF) && strcmp(qname, mi->seq[r[k]>>32].name) == 0 && rpos == (q->qpos>>1)) // avoid the diagonal
if (qname && (opt->flag&MM_F_NO_SELF) && strcmp(qname, tname) == 0 && rpos == (q->qpos>>1)) // avoid the diagonal
continue;
if (qname && (opt->flag&MM_F_AVA) && strcmp(qname, mi->seq[r[k]>>32].name) > 0) // all-vs-all mode: map once
if (qname && (opt->flag&MM_F_AVA) && strcmp(qname, tname) > 0) // all-vs-all mode: map once
continue;
p = &a[j++];
if ((r[k]&1) == (q->qpos&1)) { // forward strand
@ -259,7 +263,7 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
radix_sort_128x(a, a + n_a);
// for (i = 0; i < n_a; ++i) printf("%c\t%d\t%d\n", "+-"[a[i].x>>63], (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
t = kmalloc(b->km_fixed, (n_a + opt->min_cnt - 1) / opt->min_cnt * sizeof(int));
t = (int*)kmalloc(b->km_fixed, (n_a + opt->min_cnt - 1) / opt->min_cnt * sizeof(int));
n_t = mm_liss(opt->radius, opt->min_cnt, b->km_fixed, n_a, a, t);
int n_tot = 0, n_low = 0, s_low = 0;
@ -267,9 +271,17 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
if (m[i].n > 0) ++n_tot;
if (m[i].n > 0 && m[i].n < opt->mid_occ) ++n_low, s_low += m[i].n;
}
printf("%d\t%d\t%d\t%d\t%d", n_tot, n_low, s_low, n, n_t);
for (i = 0; i < n_t; ++i) printf("\t%d", t[i]);
printf("\n");
int off = 0, max = 0, max2 = 0, max_i = -1;
mm128_t *a_st = 0, *a_en = 0;
for (i = 0; i < n_t; ++i) {
if (t[i] > max) max2 = max, max = t[i], max_i = i, a_st = &a[off], a_en = &a[off + t[i]];
else if (t[i] > max2) max2 = t[i];
off += t[i];
}
printf("%s\t%d\t%d\t", qname, max, max2);
if (max_i >= 0) printf("%s:%d-%d", mi->seq[a_st->x<<1>>33].name, (uint32_t)a_st->x>>1, (uint32_t)(a_en-1)->x>>1);
else printf("*");
printf("\t%d\t%d\t%d\t%d\t%d\n", n_tot, n_low, s_low, n, n_t);
// free
for (i = 0; i < n; ++i)