Heng Li
parent
f35e152e99
commit
56723ad580
35
index.c
35
index.c
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@ -153,7 +153,7 @@ static void mm_idx_post(mm_idx_t *mi, int n_threads)
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typedef struct {
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int mini_batch_size, keep_name;
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uint64_t batch_size;
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uint64_t batch_size, sum_len;
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bseq_file_t *fp;
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mm_idx_t *mi;
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} pipeline_t;
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@ -179,7 +179,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
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pipeline_t *p = (pipeline_t*)shared;
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if (step == 0) { // step 0: read sequences
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step_t *s;
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if (p->mi->sum_len > p->batch_size) return 0;
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if (p->sum_len > p->batch_size) return 0;
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s = (step_t*)calloc(1, sizeof(step_t));
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s->seq = bseq_read(p->fp, p->mini_batch_size, &s->n_seq); // read a mini-batch
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if (s->seq) {
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@ -193,8 +193,8 @@ static void *worker_pipeline(void *shared, int step, void *in)
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p->mi->seq = (mm_idx_seq_t*)realloc(p->mi->seq, m * sizeof(mm_idx_seq_t));
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// make room for p->mi->S
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for (i = 0, sum_len = 0; i < s->n_seq; ++i) sum_len += s->seq[i].l_seq;
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old_max_len = (p->mi->sum_len + 7) / 8;
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max_len = (p->mi->sum_len + sum_len + 7) / 8;
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old_max_len = (p->sum_len + 7) / 8;
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max_len = (p->sum_len + sum_len + 7) / 8;
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kroundup64(old_max_len); kroundup64(max_len);
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if (old_max_len != max_len) {
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p->mi->S = (uint32_t*)realloc(p->mi->S, max_len * 4);
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@ -209,15 +209,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
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seq->name = strdup(s->seq[i].name);
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} else seq->name = 0;
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seq->len = s->seq[i].l_seq;
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seq->offset = p->mi->sum_len;
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seq->offset = p->sum_len;
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// copy the sequence
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for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
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uint64_t o = p->mi->sum_len + j;
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uint64_t o = p->sum_len + j;
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int c = seq_nt4_table[(uint8_t)s->seq[i].seq[j]];
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mm_seq4_set(p->mi->S, o, c);
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}
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// update p->mi->{sum_len,n_seq}
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p->mi->sum_len += seq->len;
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// update p->sum_len and p->mi->n_seq
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p->sum_len += seq->len;
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s->seq[i].rid = p->mi->n_seq++;
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}
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return s;
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@ -280,8 +280,10 @@ mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads)
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void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
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{
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uint64_t sum_len = 0;
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uint32_t x[5];
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int i;
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x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->is_hpc;
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fwrite(MM_IDX_MAGIC, 1, 4, fp);
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fwrite(x, 4, 5, fp);
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@ -291,6 +293,7 @@ void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
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fwrite(&l, 1, 1, fp);
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fwrite(mi->seq[i].name, 1, l, fp);
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fwrite(&mi->seq[i].len, 4, 1, fp);
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sum_len += mi->seq[i].len;
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}
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for (i = 0; i < 1<<mi->b; ++i) {
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mm_idx_bucket_t *b = &mi->B[i];
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@ -308,6 +311,8 @@ void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
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fwrite(x, 8, 2, fp);
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}
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}
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fwrite(mi->S, 4, (sum_len + 7) / 8, fp);
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fflush(fp);
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}
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mm_idx_t *mm_idx_load(FILE *fp)
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@ -315,7 +320,9 @@ mm_idx_t *mm_idx_load(FILE *fp)
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int i;
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char magic[4];
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uint32_t x[5];
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uint64_t sum_len = 0;
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mm_idx_t *mi;
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if (fread(magic, 1, 4, fp) != 4) return 0;
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if (strncmp(magic, MM_IDX_MAGIC, 4) != 0) return 0;
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if (fread(x, 4, 5, fp) != 6) return 0;
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@ -324,11 +331,13 @@ mm_idx_t *mm_idx_load(FILE *fp)
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mi->seq = (mm_idx_seq_t*)calloc(mi->n_seq, sizeof(mm_idx_seq_t));
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for (i = 0; i < mi->n_seq; ++i) {
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uint8_t l;
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mm_idx_seq_t *s = &mi->seq[i];
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fread(&l, 1, 1, fp);
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mi->seq[i].name = (char*)malloc(l + 1);
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fread(mi->seq[i].name, 1, l, fp);
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mi->seq[i].name[l] = 0;
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fread(&mi->seq[i].len, 4, 1, fp);
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s->name = (char*)malloc(l + 1);
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fread(s->name, 1, l, fp);
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s->name[l] = 0;
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fread(&s->len, 4, 1, fp);
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sum_len += s->len;
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}
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for (i = 0; i < 1<<mi->b; ++i) {
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mm_idx_bucket_t *b = &mi->B[i];
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@ -351,5 +360,7 @@ mm_idx_t *mm_idx_load(FILE *fp)
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kh_val(h, k) = x[1];
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}
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}
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mi->S = (uint32_t*)malloc((sum_len + 7) / 8 * 4);
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fread(mi->S, 4, (sum_len + 7) / 8, fp);
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return mi;
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}
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6
main.c
6
main.c
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@ -127,7 +127,11 @@ int main(int argc, char *argv[])
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
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if (fpw) mm_idx_dump(fpw, mi);
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if (fpw) {
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mm_idx_dump(fpw, mi);
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if (mm_verbose >= 2)
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fprintf(stderr, "[M::%s::%.3f*%.2f] dumpped the (partial) index to disk\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
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}
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/*
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for (i = optind + 1; i < argc; ++i)
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mm_map_file(mi, argv[i], &opt, n_threads, mini_batch_size);
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