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r367: index reader optionally writes index

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This commit is contained in:
Heng Li
2017-09-14 21:18:13 -04:00
parent eb00521d9b
commit e2823d4aee
5 changed files with 83 additions and 90 deletions
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index.c
+15 -2
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@@ -21,6 +21,13 @@ 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))
typedef struct mm_idx_bucket_s {
mm128_v a; // (minimizer, position) array
int32_t n; // size of the _p_ array
uint64_t *p; // position array for minimizers appearing >1 times
void *h; // hash table indexing _p_ and minimizers appearing once
} mm_idx_bucket_t;
void mm_idxopt_init(mm_idxopt_t *opt)
{
memset(opt, 0, sizeof(mm_idxopt_t));
@@ -439,7 +446,7 @@ int mm_idx_is_idx(const char *fn)
return is_idx;
}
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt)
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out)
{
int is_idx;
mm_idx_reader_t *r;
@@ -450,6 +457,7 @@ mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt)
r->opt = *opt;
if (r->is_idx) r->fp.idx = fopen(fn, "rb");
else r->fp.seq = mm_bseq_open(fn);
if (fn_out) r->fp_out = fopen(fn_out, "wb");
return r;
}
@@ -457,6 +465,8 @@ 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);
if (r->fp_out) fclose(r->fp_out);
free(r);
}
mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
@@ -468,6 +478,9 @@ mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
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;
if (mi) {
if (r->fp_out) mm_idx_dump(r->fp_out, mi);
++r->n_parts;
}
return mi;
}