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r188: renamed bseq* to mm_bseq*

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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
This commit is contained in:
Heng Li
2017-07-19 09:26:46 -04:00
parent b9b0b6f49c
commit 71c988f6ab
10 changed files with 65 additions and 57 deletions
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map.c
+6 -6
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@@ -281,7 +281,7 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, m
typedef struct {
int mini_batch_size, n_processed, n_threads;
const mm_mapopt_t *opt;
bseq_file_t *fp;
mm_bseq_file_t *fp;
const mm_idx_t *mi;
kstring_t str;
} pipeline_t;
@@ -289,7 +289,7 @@ typedef struct {
typedef struct {
const pipeline_t *p;
int n_seq;
bseq1_t *seq;
mm_bseq1_t *seq;
int *n_reg;
mm_reg1_t **reg;
mm_tbuf_t **buf;
@@ -311,7 +311,7 @@ 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 = bseq_read(p->fp, p->mini_batch_size, with_qual, &s->n_seq);
s->seq = mm_bseq_read(p->fp, p->mini_batch_size, with_qual, &s->n_seq);
if (s->seq) {
s->p = p;
for (i = 0; i < s->n_seq; ++i)
@@ -332,7 +332,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
free(s->buf);
for (i = 0; i < s->n_seq; ++i) {
bseq1_t *t = &s->seq[i];
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r);
@@ -360,7 +360,7 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
{
pipeline_t pl;
memset(&pl, 0, sizeof(pipeline_t));
pl.fp = bseq_open(fn);
pl.fp = mm_bseq_open(fn);
if (pl.fp == 0) return -1;
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
@@ -371,6 +371,6 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
}
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
free(pl.str.s);
bseq_close(pl.fp);
mm_bseq_close(pl.fp);
return 0;
}