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working with toy examples

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This commit is contained in:
Heng Li
2018-07-15 10:55:00 -04:00
parent 951c0d1d35
commit 4b707aac92
5 changed files with 49 additions and 34 deletions
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map.c
+20 -4
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@@ -399,6 +399,7 @@ typedef struct {
kstring_t str;
int n_parts;
uint32_t *rid_shift;
FILE *fp_split, **fp_parts;
} pipeline_t;
@@ -486,6 +487,7 @@ static void merge_hits(step_t *s)
mm_reg1_t *r = &s->reg[k][l];
uint32_t capacity;
mm_err_fread(r, sizeof(mm_reg1_t), 1, fp[j]);
r->rid += s->p->rid_shift[j];
if (opt->flag & MM_F_CIGAR) {
mm_err_fread(&capacity, 4, 1, fp[j]);
r->p = (mm_extra_t*)calloc(capacity, 4);
@@ -494,6 +496,7 @@ static void merge_hits(step_t *s)
}
}
}
mm_hit_sort(km, &s->n_reg[k], s->reg[k]);
mm_set_parent(km, opt->mask_level, s->n_reg[k], s->reg[k], opt->a * 2 + opt->b);
if (!(opt->flag & MM_F_ALL_CHAINS)) {
mm_select_sub(km, opt->pri_ratio, s->p->mi->k*2, opt->best_n, &s->n_reg[k], s->reg[k]);
@@ -663,13 +666,26 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
pl.fp = open_bseqs(pl.n_fp, fn);
if (pl.fp == 0) return -1;
pl.opt = opt;
pl.n_parts = n_split_idx;
pl.fp_parts = mm_split_merge_prep(opt->split_prefix, n_split_idx, &mi);
if (pl.fp_parts == 0) return -1;
pl.mi = mi;
pl.mini_batch_size = opt->mini_batch_size;
pl.n_parts = n_split_idx;
pl.fp_parts = CALLOC(FILE*, pl.n_parts);
pl.rid_shift = CALLOC(uint32_t, pl.n_parts);
pl.mi = mm_split_merge_prep(opt->split_prefix, n_split_idx, pl.fp_parts, pl.rid_shift);
if (pl.mi == 0) {
free(pl.fp_parts);
free(pl.rid_shift);
return -1;
}
for (i = n_split_idx - 1; i > 0; --i)
pl.rid_shift[i] = pl.rid_shift[i - 1];
for (pl.rid_shift[0] = 0, i = 1; i < n_split_idx; ++i)
pl.rid_shift[i] += pl.rid_shift[i - 1];
kt_pipeline(2, worker_pipeline, &pl, 3);
free(pl.str.s);
free(pl.rid_shift);
for (i = 0; i < n_split_idx; ++i)
fclose(pl.fp_parts[i]);
free(pl.fp_parts);