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redesigned indexing and option APIs

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This commit is contained in:
Heng Li
2017-09-14 17:02:01 -04:00
parent 0f7455cefa
commit eb00521d9b
5 changed files with 151 additions and 98 deletions
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index.c
+43 -1
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@@ -21,6 +21,15 @@ 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))
void mm_idxopt_init(mm_idxopt_t *opt)
{
memset(opt, 0, sizeof(mm_idxopt_t));
opt->k = 15, opt->w = 10, opt->is_hpc = 0;
opt->bucket_bits = 14;
opt->mini_batch_size = 50000000;
opt->batch_size = 4000000000ULL;
}
mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc)
{
mm_idx_t *mi;
@@ -314,7 +323,7 @@ mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads)
mm_idx_t *mi;
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);
mi = mm_idx_gen(fp, w, k, 14, is_hpc, 1<<18, n_threads, UINT64_MAX, 1);
mm_bseq_close(fp);
return mi;
}
@@ -429,3 +438,36 @@ int mm_idx_is_idx(const char *fn)
close(fd);
return is_idx;
}
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt)
{
int is_idx;
mm_idx_reader_t *r;
is_idx = mm_idx_is_idx(fn);
if (is_idx < 0) return 0; // failed to open the index
r = (mm_idx_reader_t*)calloc(1, sizeof(mm_idx_reader_t));
r->is_idx = is_idx;
r->opt = *opt;
if (r->is_idx) r->fp.idx = fopen(fn, "rb");
else r->fp.seq = mm_bseq_open(fn);
return r;
}
void mm_idx_reader_close(mm_idx_reader_t *r)
{
if (r->is_idx) fclose(r->fp.idx);
else mm_bseq_close(r->fp.seq);
}
mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
{
mm_idx_t *mi;
if (r->is_idx) {
mi = mm_idx_load(r->fp.idx);
if (mi && mm_verbose >= 2 && (mi->k != r->opt.k || mi->w != r->opt.w || mi->is_hpc != r->opt.is_hpc))
fprintf(stderr, "[WARNING] Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index.\n");
} else
mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.is_hpc, r->opt.mini_batch_size, n_threads, r->opt.batch_size, 1);
if (mi) ++r->n_parts;
return mi;
}