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is_hpc is a property of the index

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This commit is contained in:
Heng Li
2017-04-07 15:42:33 -04:00
parent b3bc4911ba
commit f5cdd3f72f
4 changed files with 158 additions and 15 deletions
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index.c
+11 -12
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@@ -14,13 +14,13 @@ typedef khash_t(idx) idxhash_t;
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
mm_idx_t *mm_idx_init(int w, int k, int b)
mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc)
{
mm_idx_t *mi;
if (k*2 < b) b = k * 2;
if (w < 1) w = 1;
mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t));
mi->w = w, mi->k = k, mi->b = b;
mi->w = w, mi->k = k, mi->b = b, mi->is_hpc = is_hpc;
mi->B = (mm_idx_bucket_t*)calloc(1<<b, sizeof(mm_idx_bucket_t));
return mi;
}
@@ -151,7 +151,7 @@ static void mm_idx_post(mm_idx_t *mi, int n_threads)
#include "bseq.h"
typedef struct {
int mini_batch_size, keep_name, is_hpc;
int mini_batch_size, keep_name;
uint64_t batch_size;
bseq_file_t *fp;
mm_idx_t *mi;
@@ -225,7 +225,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
step_t *s = (step_t*)in;
for (i = 0; i < s->n_seq; ++i) {
bseq1_t *t = &s->seq[i];
mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->is_hpc, &s->a);
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);
}
free(s->seq); s->seq = 0;
@@ -244,11 +244,10 @@ mm_idx_t *mm_idx_gen(bseq_file_t *fp, int w, int k, int b, int is_hpc, int mini_
memset(&pl, 0, sizeof(pipeline_t));
pl.mini_batch_size = mini_batch_size;
pl.keep_name = keep_name;
pl.is_hpc = is_hpc;
pl.batch_size = batch_size;
pl.fp = fp;
if (pl.fp == 0) return 0;
pl.mi = mm_idx_init(w, k, b);
pl.mi = mm_idx_init(w, k, b, is_hpc);
kt_pipeline(n_threads < 3? n_threads : 3, worker_pipeline, &pl, 3);
if (mm_verbose >= 3)
@@ -280,11 +279,11 @@ mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads)
void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
{
uint32_t x[4];
uint32_t x[5];
int i;
x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq;
x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->is_hpc;
fwrite(MM_IDX_MAGIC, 1, 4, fp);
fwrite(x, 4, 4, fp);
fwrite(x, 4, 5, fp);
for (i = 0; i < mi->n_seq; ++i) {
uint8_t l;
l = strlen(mi->seq[i].name);
@@ -314,12 +313,12 @@ mm_idx_t *mm_idx_load(FILE *fp)
{
int i;
char magic[4];
uint32_t x[4];
uint32_t x[5];
mm_idx_t *mi;
if (fread(magic, 1, 4, fp) != 4) return 0;
if (strncmp(magic, MM_IDX_MAGIC, 4) != 0) return 0;
if (fread(x, 4, 4, fp) != 6) return 0;
mi = mm_idx_init(x[0], x[1], x[2]);
if (fread(x, 4, 5, fp) != 6) return 0;
mi = mm_idx_init(x[0], x[1], x[2], x[4]);
mi->n_seq = x[3];
mi->seq = (mm_idx_seq_t*)calloc(mi->n_seq, sizeof(mm_idx_seq_t));
for (i = 0; i < mi->n_seq; ++i) {