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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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index.c
+8 -8
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@@ -190,13 +190,13 @@ static void mm_idx_post(mm_idx_t *mi, int n_threads)
typedef struct {
int mini_batch_size, keep_name;
uint64_t batch_size, sum_len;
bseq_file_t *fp;
mm_bseq_file_t *fp;
mm_idx_t *mi;
} pipeline_t;
typedef struct {
int n_seq;
bseq1_t *seq;
mm_bseq1_t *seq;
mm128_v a;
} step_t;
@@ -217,7 +217,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
step_t *s;
if (p->sum_len > p->batch_size) return 0;
s = (step_t*)calloc(1, sizeof(step_t));
s->seq = bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
s->seq = mm_bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
if (s->seq) {
uint32_t old_m, m;
uint64_t sum_len, old_max_len, max_len;
@@ -261,7 +261,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
} else if (step == 1) { // step 1: compute sketch
step_t *s = (step_t*)in;
for (i = 0; i < s->n_seq; ++i) {
bseq1_t *t = &s->seq[i];
mm_bseq1_t *t = &s->seq[i];
mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->is_hpc, &s->a);
free(t->seq); free(t->name);
}
@@ -275,7 +275,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
return 0;
}
mm_idx_t *mm_idx_gen(bseq_file_t *fp, int w, int k, int b, int is_hpc, int mini_batch_size, int n_threads, uint64_t batch_size, int keep_name)
mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int is_hpc, int mini_batch_size, int n_threads, uint64_t batch_size, int keep_name)
{
pipeline_t pl;
memset(&pl, 0, sizeof(pipeline_t));
@@ -299,12 +299,12 @@ mm_idx_t *mm_idx_gen(bseq_file_t *fp, int w, int k, int b, int is_hpc, int mini_
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads) // a simpler interface
{
bseq_file_t *fp;
mm_bseq_file_t *fp;
mm_idx_t *mi;
fp = bseq_open(fn);
fp = mm_bseq_open(fn);
if (fp == 0) return 0;
mi = mm_idx_gen(fp, w, k, MM_IDX_DEF_B, is_hpc, 1<<18, n_threads, UINT64_MAX, 1);
bseq_close(fp);
mm_bseq_close(fp);
return mi;
}