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mostly debugging code

This commit is contained in:
Heng Li 2017-05-01 16:50:09 +08:00
parent 2c9f1bce3e
commit f2ae8eb670
2 changed files with 22 additions and 10 deletions
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5
main.c
View File

@ -25,7 +25,6 @@ int main(int argc, char *argv[])
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 mini_batch_size = 100000000;
uint64_t batch_size = 4000000000ULL;
float f = 0.001;
bseq_file_t *fp = 0;
char *fnw = 0;
FILE *fpr = 0, *fpw = 0;
@ -43,7 +42,7 @@ int main(int argc, char *argv[])
else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
else if (c == 'r') opt.radius = atoi(optarg);
else if (c == 'c') opt.min_cnt = atoi(optarg);
else if (c == 'f') f = atof(optarg);
else if (c == 'f') opt.mid_occ_frac = atof(optarg);
else if (c == 't') n_threads = atoi(optarg);
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = atoi(optarg);
@ -87,7 +86,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -l the 1st argument is a index file (overriding -k, -w and -I)\n");
// fprintf(stderr, " -b INT bucket bits [%d]\n", b); // most users wouldn't care about this
fprintf(stderr, " Mapping:\n");
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", f);
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac);
fprintf(stderr, " -r INT bandwidth [%d]\n", opt.radius);
fprintf(stderr, " -c INT retain a mapping if it consists of >=INT minimizers [%d]\n", opt.min_cnt);
fprintf(stderr, " -L INT min matching length [%d]\n", opt.min_match);

27
map.c
View File

@ -11,7 +11,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
{
opt->n_frag_mini = 100;
opt->max_occ_frac = 1e-5f;
opt->mid_occ_frac = 1e-3f;
opt->mid_occ_frac = 2e-4f;
opt->sdust_thres = 0;
opt->radius = 500;
@ -108,7 +108,7 @@ int mm_pair_thin_core(mm_tbuf_t *b, uint64_t x, int radius, int rel, int st0, in
for (i = st; i < en; ++i) {
uint64_t y = z[i];
if (((x ^ y) & 1) == rel) {
printf("* %d,%d\n", (uint32_t)x>>1, (uint32_t)y>>1);
// printf("* %d,%d\n", (uint32_t)x>>1, (uint32_t)y>>1);
kv_push(uint64_t, b->km_fixed, *a, y);
}
}
@ -148,7 +148,7 @@ void mm_pair_thin(mm_tbuf_t *b, int radius, mm_match_t *m1, mm_match_t *m2)
}
for (i = 0; i < 2; ++i)
m[i]->n = a[i].n, m[i]->x.r = a[i].a, m[i]->is_alloc = 1;
printf("%d,%d; %d,%d\n", m[0]->qpos>>1, m[1]->qpos>>1, m[0]->n, m[1]->n);
// printf("%d,%d; %d,%d\n", m[0]->qpos>>1, m[1]->qpos>>1, m[0]->n, m[1]->n);
}
void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint32_t m_st, uint32_t m_en)
@ -167,8 +167,10 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
m[i].span = p->x & 0xff;
m[i].x.cr = mm_idx_get(mi, p->x>>8, &t);
m[i].n = t;
if (i) printf("; ");
if (mm_verbose >= 5) printf("%d,%d", m[i].qpos>>1, t);
if (mm_verbose >= 5) {
if (i) printf("; ");
printf("%d,%d", m[i].qpos>>1, t);
}
}
if (mm_verbose >= 5) printf("\n");
@ -178,15 +180,26 @@ 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) {
if (last2 < 0) last2 = i;
if (last < 0 || m[last].n < m[i].n) last = i;
if (last >= 0 && (m[last].qpos>>1) + (m[last].span>>1) <= m[i].qpos>>1) {
if (last >= 0 && (m[last].qpos>>1) + (m[last].span>>0) <= m[i].qpos>>1) {
mm_pair_thin(b, opt->radius, &m[last], &m[i]);
last2 = last = -1;
} else if (last2 >= 0 && (m[last2].qpos>>1) + (m[last2].span>>1) <= m[i].qpos>>1) {
} else if (last2 >= 0 && (m[last2].qpos>>1) + (m[last2].span>>0) <= m[i].qpos>>1) {
mm_pair_thin(b, opt->radius, &m[last2], &m[i]);
last2 = last = -1;
}
}
}
int n_tot = 0, n_low = 0, s_low = 0;
for (i = 0; i < n; ++i) {
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\n", n_tot, n_low, s_low, n);
// free
for (i = 0; i < n; ++i)
if (m[i].is_alloc) kfree(b->km_fixed, m[i].x.r);
kfree(b->km_fixed, m);
}