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allow to read multiple files interleaved

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This commit is contained in:
Heng Li
2017-09-24 14:33:05 -04:00
parent 84bbc47152
commit f0951141a1
4 changed files with 66 additions and 15 deletions
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map.c
+30 -13
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@@ -317,18 +317,18 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm
**************************/
typedef struct {
int mini_batch_size, n_processed, n_threads;
int mini_batch_size, n_processed, n_threads, n_fp;
const mm_mapopt_t *opt;
mm_bseq_file_t *fp;
mm_bseq_file_t **fp;
const mm_idx_t *mi;
kstring_t str;
} pipeline_t;
typedef struct {
const pipeline_t *p;
int n_seq;
int n_seq, n_frag;
mm_bseq1_t *seq;
int *n_reg;
int *n_reg, *n_seg;
mm_reg1_t **reg;
mm_tbuf_t **buf;
} step_t;
@@ -349,7 +349,8 @@ static void *worker_pipeline(void *shared, int step, void *in)
int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
step_t *s;
s = (step_t*)calloc(1, sizeof(step_t));
s->seq = mm_bseq_read(p->fp, p->mini_batch_size, with_qual, &s->n_seq);
if (p->n_fp > 1) s->seq = mm_bseq_read_multi(p->n_fp, p->fp, p->mini_batch_size, with_qual, &s->n_seq);
else s->seq = mm_bseq_read2(p->fp[0], p->mini_batch_size, with_qual, !!(p->opt->flag&MM_F_MULTI_SEG), &s->n_seq);
if (s->seq) {
s->p = p;
for (i = 0; i < s->n_seq; ++i)
@@ -399,22 +400,38 @@ static void *worker_pipeline(void *shared, int step, void *in)
return 0;
}
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads)
int mm_map_file_multi_seg(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads)
{
int i, j;
pipeline_t pl;
if (n_segs < 1) return -1;
memset(&pl, 0, sizeof(pipeline_t));
pl.fp = mm_bseq_open(fn);
if (pl.fp == 0) {
if (mm_verbose >= 1)
fprintf(stderr, "ERROR: failed to open file '%s'\n", fn);
return -1;
pl.fp = (mm_bseq_file_t**)calloc(n_segs, sizeof(mm_bseq_file_t*));
for (i = 0; i < n_segs; ++i) {
pl.fp[i] = mm_bseq_open(fn[i]);
if (pl.fp[i] == 0) {
if (mm_verbose >= 1)
fprintf(stderr, "ERROR: failed to open file '%s'\n", fn[i]);
for (j = 0; j < i; ++j)
mm_bseq_close(pl.fp[j]);
free(pl.fp);
return -1;
}
}
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads, pl.mini_batch_size = opt->mini_batch_size;
pl.n_threads = n_threads > 1? n_threads : 1;
pl.mini_batch_size = opt->mini_batch_size;
if ((opt->flag & MM_F_OUT_SAM) && !(opt->flag & MM_F_NO_SAM_SQ))
mm_write_sam_SQ(idx);
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
free(pl.str.s);
mm_bseq_close(pl.fp);
for (i = 0; i < n_segs; ++i)
mm_bseq_close(pl.fp[i]);
free(pl.fp);
return 0;
}
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads)
{
return mm_map_file_multi_seg(idx, 1, &fn, opt, n_threads);
}