402 lines
11 KiB
C
402 lines
11 KiB
C
#include <stdlib.h>
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#include <assert.h>
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#include <stdio.h>
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#include "kthread.h"
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#include "bseq.h"
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#include "minimap.h"
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#include "mmpriv.h"
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#include "kvec.h"
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#include "khash.h"
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#define idx_hash(a) ((a)>>1)
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#define idx_eq(a, b) ((a)>>1 == (b)>>1)
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KHASH_INIT(idx, uint64_t, uint64_t, 1, idx_hash, idx_eq)
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typedef khash_t(idx) idxhash_t;
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#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
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mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc)
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{
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mm_idx_t *mi;
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if (k*2 < b) b = k * 2;
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if (w < 1) w = 1;
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mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t));
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mi->w = w, mi->k = k, mi->b = b, mi->is_hpc = is_hpc;
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mi->B = (mm_idx_bucket_t*)calloc(1<<b, sizeof(mm_idx_bucket_t));
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return mi;
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}
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void mm_idx_destroy(mm_idx_t *mi)
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{
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int i;
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if (mi == 0) return;
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for (i = 0; i < 1<<mi->b; ++i) {
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free(mi->B[i].p);
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free(mi->B[i].a.a);
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kh_destroy(idx, (idxhash_t*)mi->B[i].h);
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}
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for (i = 0; i < mi->n_seq; ++i)
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free(mi->seq[i].name);
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free(mi->seq); free(mi->B); free(mi->S); free(mi);
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}
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const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
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{
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int mask = (1<<mi->b) - 1;
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khint_t k;
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mm_idx_bucket_t *b = &mi->B[minier&mask];
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idxhash_t *h = (idxhash_t*)b->h;
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*n = 0;
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if (h == 0) return 0;
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k = kh_get(idx, h, minier>>mi->b<<1);
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if (k == kh_end(h)) return 0;
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if (kh_key(h, k)&1) { // special casing when there is only one k-mer
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*n = 1;
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return &kh_val(h, k);
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} else {
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*n = (uint32_t)kh_val(h, k);
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return &b->p[kh_val(h, k)>>32];
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}
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}
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void mm_idx_stat(const mm_idx_t *mi)
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{
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int i, n = 0, n1 = 0;
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uint64_t sum = 0, len = 0;
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fprintf(stderr, "[M::%s] kmer size: %d; skip: %d; is_HPC: %d; #seq: %d\n", __func__, mi->k, mi->w, mi->is_hpc, mi->n_seq);
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for (i = 0; i < mi->n_seq; ++i)
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len += mi->seq[i].len;
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for (i = 0; i < 1<<mi->b; ++i)
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if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
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for (i = 0; i < 1<<mi->b; ++i) {
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idxhash_t *h = (idxhash_t*)mi->B[i].h;
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khint_t k;
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if (h == 0) continue;
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for (k = 0; k < kh_end(h); ++k)
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if (kh_exist(h, k)) {
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sum += kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
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if (kh_key(h, k)&1) ++n1;
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}
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}
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fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf\n",
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum);
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}
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int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
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{
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uint64_t i, st1, en1;
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if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
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if (en > mi->seq[rid].len) en = mi->seq[rid].len;
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st1 = mi->seq[rid].offset + st;
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en1 = mi->seq[rid].offset + en;
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for (i = st1; i < en1; ++i)
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seq[i - st1] = mm_seq4_get(mi->S, i);
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return en - st;
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}
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uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
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{
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int i;
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size_t n = 0;
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uint32_t thres;
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khint_t *a, k;
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if (f <= 0.) return UINT32_MAX;
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for (i = 0; i < 1<<mi->b; ++i)
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if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
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a = (uint32_t*)malloc(n * 4);
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for (i = n = 0; i < 1<<mi->b; ++i) {
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idxhash_t *h = (idxhash_t*)mi->B[i].h;
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if (h == 0) continue;
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for (k = 0; k < kh_end(h); ++k) {
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if (!kh_exist(h, k)) continue;
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a[n++] = kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
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}
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}
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thres = ks_ksmall_uint32_t(n, a, (uint32_t)((1. - f) * n)) + 1;
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free(a);
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return thres;
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}
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/*********************************
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* Sort and generate hash tables *
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*********************************/
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static void worker_post(void *g, long i, int tid)
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{
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int j, start_a, start_p, n, n_keys;
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idxhash_t *h;
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mm_idx_t *mi = (mm_idx_t*)g;
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mm_idx_bucket_t *b = &mi->B[i];
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if (b->a.n == 0) return;
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// sort by minimizer
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radix_sort_128x(b->a.a, b->a.a + b->a.n);
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// count and preallocate
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for (j = 1, n = 1, n_keys = 0, b->n = 0; j <= b->a.n; ++j) {
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if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
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++n_keys;
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if (n > 1) b->n += n;
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n = 1;
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} else ++n;
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}
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h = kh_init(idx);
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kh_resize(idx, h, n_keys);
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b->p = (uint64_t*)calloc(b->n, 8);
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// create the hash table
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for (j = 1, n = 1, start_a = start_p = 0; j <= b->a.n; ++j) {
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if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
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khint_t itr;
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int absent;
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mm128_t *p = &b->a.a[j-1];
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itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
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assert(absent && j - start_a == n);
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if (n == 1) {
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kh_key(h, itr) |= 1;
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kh_val(h, itr) = p->y;
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} else {
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int k;
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for (k = 0; k < n; ++k)
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b->p[start_p + k] = b->a.a[start_a + k].y;
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radix_sort_64(&b->p[start_p], &b->p[start_p + n]); // sort by position; needed as in-place radix_sort_128x() is not stable
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kh_val(h, itr) = (uint64_t)start_p<<32 | n;
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start_p += n;
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}
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start_a = j, n = 1;
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} else ++n;
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}
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b->h = h;
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assert(b->n == start_p);
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// deallocate and clear b->a
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free(b->a.a);
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b->a.n = b->a.m = 0, b->a.a = 0;
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}
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static void mm_idx_post(mm_idx_t *mi, int n_threads)
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{
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kt_for(n_threads, worker_post, mi, 1<<mi->b);
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}
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/******************
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* Generate index *
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******************/
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#include <string.h>
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#include <zlib.h>
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#include "bseq.h"
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typedef struct {
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int mini_batch_size, keep_name;
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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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typedef struct {
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int n_seq;
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bseq1_t *seq;
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mm128_v a;
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} step_t;
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static void mm_idx_add(mm_idx_t *mi, int n, const mm128_t *a)
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{
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int i, mask = (1<<mi->b) - 1;
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for (i = 0; i < n; ++i) {
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mm128_v *p = &mi->B[a[i].x>>8&mask].a;
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kv_push(mm128_t, 0, *p, a[i]);
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}
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}
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static void *worker_pipeline(void *shared, int step, void *in)
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{
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int i;
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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->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, 0, &s->n_seq); // read a mini-batch
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if (s->seq) {
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uint32_t old_m, m;
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uint64_t sum_len, old_max_len, max_len;
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assert((uint64_t)p->mi->n_seq + s->n_seq <= UINT32_MAX); // to prevent integer overflow
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// make room for p->mi->seq
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old_m = p->mi->n_seq, m = p->mi->n_seq + s->n_seq;
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kroundup32(m); kroundup32(old_m);
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if (old_m != m)
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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->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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memset(&p->mi->S[old_max_len], 0, 4 * (max_len - old_max_len));
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}
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// populate p->mi->seq
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for (i = 0; i < s->n_seq; ++i) {
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mm_idx_seq_t *seq = &p->mi->seq[p->mi->n_seq];
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uint32_t j;
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if (p->keep_name) {
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assert(strlen(s->seq[i].name) <= 254); // a long query name breaks BAM
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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->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->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->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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} else free(s);
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} else if (step == 1) { // step 1: compute sketch
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step_t *s = (step_t*)in;
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for (i = 0; i < s->n_seq; ++i) {
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bseq1_t *t = &s->seq[i];
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mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->is_hpc, &s->a);
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free(t->seq); free(t->name);
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}
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free(s->seq); s->seq = 0;
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return s;
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} else if (step == 2) { // dispatch sketch to buckets
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step_t *s = (step_t*)in;
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mm_idx_add(p->mi, s->a.n, s->a.a);
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free(s->a.a); free(s);
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}
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return 0;
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}
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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)
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{
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pipeline_t pl;
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memset(&pl, 0, sizeof(pipeline_t));
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pl.mini_batch_size = mini_batch_size;
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pl.keep_name = keep_name;
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pl.batch_size = batch_size;
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pl.fp = fp;
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if (pl.fp == 0) return 0;
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pl.mi = mm_idx_init(w, k, b, is_hpc);
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kt_pipeline(n_threads < 3? n_threads : 3, worker_pipeline, &pl, 3);
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] collected minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
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mm_idx_post(pl.mi, n_threads);
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] sorted minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
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return pl.mi;
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}
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mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads) // a simpler interface
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{
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bseq_file_t *fp;
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mm_idx_t *mi;
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fp = bseq_open(fn);
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if (fp == 0) return 0;
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mi = mm_idx_gen(fp, w, k, MM_IDX_DEF_B, is_hpc, 1<<18, n_threads, UINT64_MAX, 1);
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bseq_close(fp);
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return mi;
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}
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/*************
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* index I/O *
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*************/
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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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for (i = 0; i < mi->n_seq; ++i) {
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uint8_t l;
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l = strlen(mi->seq[i].name);
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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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khint_t k;
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idxhash_t *h = (idxhash_t*)b->h;
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uint32_t size = h? h->size : 0;
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fwrite(&b->n, 4, 1, fp);
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fwrite(b->p, 8, b->n, fp);
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fwrite(&size, 4, 1, fp);
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if (size == 0) continue;
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for (k = 0; k < kh_end(h); ++k) {
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uint64_t x[2];
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if (!kh_exist(h, k)) continue;
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x[0] = kh_key(h, k), x[1] = kh_val(h, k);
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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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{
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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) != 5) return 0;
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mi = mm_idx_init(x[0], x[1], x[2], x[4]);
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mi->n_seq = x[3];
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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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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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s->offset = sum_len;
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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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uint32_t j, size;
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khint_t k;
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idxhash_t *h;
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fread(&b->n, 4, 1, fp);
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b->p = (uint64_t*)malloc(b->n * 8);
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fread(b->p, 8, b->n, fp);
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fread(&size, 4, 1, fp);
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if (size == 0) continue;
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b->h = h = kh_init(idx);
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kh_resize(idx, h, size);
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for (j = 0; j < size; ++j) {
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uint64_t x[2];
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int absent;
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fread(x, 8, 2, fp);
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k = kh_put(idx, h, x[0], &absent);
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assert(absent);
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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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