575 lines
16 KiB
C
575 lines
16 KiB
C
#include <stdlib.h>
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#include <assert.h>
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#if defined(WIN32) || defined(_WIN32)
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#include <io.h> // for open(2)
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#else
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#include <unistd.h>
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#endif
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#include <fcntl.h>
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#include <stdio.h>
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#define __STDC_LIMIT_MACROS
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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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KHASH_MAP_INIT_STR(str, uint32_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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typedef struct mm_idx_bucket_s {
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mm128_v a; // (minimizer, position) array
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int32_t n; // size of the _p_ array
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uint64_t *p; // position array for minimizers appearing >1 times
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void *h; // hash table indexing _p_ and minimizers appearing once
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} mm_idx_bucket_t;
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mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
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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->flag = flag;
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mi->B = (mm_idx_bucket_t*)calloc(1<<b, sizeof(mm_idx_bucket_t));
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if (!(mm_dbg_flag & 1)) mi->km = km_init();
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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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uint32_t i;
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if (mi == 0) return;
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if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
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for (i = 0; i < 1U<<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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if (!mi->km) {
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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);
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} else km_destroy(mi->km);
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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 n = 0, n1 = 0;
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uint32_t i;
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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->flag&MM_I_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 < 1U<<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 < 1U<<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_index_name(mm_idx_t *mi)
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{
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khash_t(str) *h;
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uint32_t i;
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int has_dup = 0, absent;
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if (mi->h) return 0;
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h = kh_init(str);
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for (i = 0; i < mi->n_seq; ++i) {
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khint_t k;
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k = kh_put(str, h, mi->seq[i].name, &absent);
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if (absent) kh_val(h, k) = i;
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else has_dup = 1;
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}
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mi->h = h;
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if (has_dup && mm_verbose >= 2)
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fprintf(stderr, "[WARNING] some database sequences have identical sequence names\n");
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return has_dup;
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}
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int mm_idx_name2id(const mm_idx_t *mi, const char *name)
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{
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khash_t(str) *h = (khash_t(str)*)mi->h;
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khint_t k;
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if (h == 0) return -2;
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k = kh_get(str, h, name);
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return k == kh_end(h)? -1 : kh_val(h, k);
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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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int32_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 INT32_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 n, n_keys;
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size_t j, start_a, start_p;
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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 == (int32_t)start_p);
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// deallocate and clear b->a
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kfree(0, 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;
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uint64_t batch_size, sum_len;
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mm_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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mm_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 = mm_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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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*)krealloc(p->mi->km, p->mi->seq, m * sizeof(mm_idx_seq_t));
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// make room for p->mi->S
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if (!(p->mi->flag & MM_I_NO_SEQ)) {
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uint64_t sum_len, old_max_len, max_len;
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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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}
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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->mi->flag & MM_I_NO_NAME)) {
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seq->name = (char*)kmalloc(p->mi->km, strlen(s->seq[i].name) + 1);
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strcpy(seq->name, 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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if (!(p->mi->flag & MM_I_NO_SEQ)) {
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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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}
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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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mm_bseq1_t *t = &s->seq[i];
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if (t->l_seq > 0)
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mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->flag&MM_I_HPC, &s->a);
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else if (mm_verbose >= 2)
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fprintf(stderr, "[WARNING] the length database sequence '%s' is 0\n", t->name);
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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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kfree(0, 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(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini_batch_size, int n_threads, uint64_t batch_size)
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{
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pipeline_t pl;
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if (fp == 0 || mm_bseq_eof(fp)) return 0;
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memset(&pl, 0, sizeof(pipeline_t));
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pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
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pl.batch_size = batch_size;
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pl.fp = fp;
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pl.mi = mm_idx_init(w, k, b, flag);
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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 flag, int n_threads) // a simpler interface; deprecated
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{
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mm_bseq_file_t *fp;
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mm_idx_t *mi;
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fp = mm_bseq_open(fn);
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if (fp == 0) return 0;
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mi = mm_idx_gen(fp, w, k, 14, flag, 1<<18, n_threads, UINT64_MAX);
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mm_bseq_close(fp);
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return mi;
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}
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mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const char **seq, const char **name)
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{
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uint64_t sum_len = 0;
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mm128_v a = {0,0,0};
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mm_idx_t *mi;
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int i, flag = 0;
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if (n <= 0) return 0;
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for (i = 0; i < n; ++i) // get the total length
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sum_len += strlen(seq[i]);
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if (is_hpc) flag |= MM_I_HPC;
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if (name == 0) flag |= MM_I_NO_NAME;
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if (bucket_bits < 0) bucket_bits = 14;
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mi = mm_idx_init(w, k, bucket_bits, flag);
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mi->n_seq = n;
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mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, n, sizeof(mm_idx_seq_t)); // ->seq is allocated from km
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mi->S = (uint32_t*)calloc((sum_len + 7) / 8, 4);
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for (i = 0, sum_len = 0; i < n; ++i) {
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const char *s = seq[i];
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mm_idx_seq_t *p = &mi->seq[i];
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uint32_t j;
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if (name && name[i]) {
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p->name = (char*)kmalloc(mi->km, strlen(name[i]) + 1);
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strcpy(p->name, name[i]);
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}
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p->offset = sum_len;
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p->len = strlen(s);
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for (j = 0; j < p->len; ++j) {
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int c = seq_nt4_table[(uint8_t)s[j]];
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uint64_t o = sum_len + j;
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mm_seq4_set(mi->S, o, c);
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}
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sum_len += p->len;
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if (p->len > 0) {
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a.n = 0;
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mm_sketch(0, s, p->len, w, k, i, is_hpc, &a);
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mm_idx_add(mi, a.n, a.a);
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}
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}
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free(a.a);
|
|
mm_idx_post(mi, 1);
|
|
return mi;
|
|
}
|
|
|
|
/*************
|
|
* index I/O *
|
|
*************/
|
|
|
|
void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
|
|
{
|
|
uint64_t sum_len = 0;
|
|
uint32_t x[5], i;
|
|
|
|
x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->flag;
|
|
fwrite(MM_IDX_MAGIC, 1, 4, fp);
|
|
fwrite(x, 4, 5, fp);
|
|
for (i = 0; i < mi->n_seq; ++i) {
|
|
if (mi->seq[i].name) {
|
|
uint8_t l = strlen(mi->seq[i].name);
|
|
fwrite(&l, 1, 1, fp);
|
|
fwrite(mi->seq[i].name, 1, l, fp);
|
|
} else {
|
|
uint8_t l = 0;
|
|
fwrite(&l, 1, 1, fp);
|
|
}
|
|
fwrite(&mi->seq[i].len, 4, 1, fp);
|
|
sum_len += mi->seq[i].len;
|
|
}
|
|
for (i = 0; i < 1<<mi->b; ++i) {
|
|
mm_idx_bucket_t *b = &mi->B[i];
|
|
khint_t k;
|
|
idxhash_t *h = (idxhash_t*)b->h;
|
|
uint32_t size = h? h->size : 0;
|
|
fwrite(&b->n, 4, 1, fp);
|
|
fwrite(b->p, 8, b->n, fp);
|
|
fwrite(&size, 4, 1, fp);
|
|
if (size == 0) continue;
|
|
for (k = 0; k < kh_end(h); ++k) {
|
|
uint64_t x[2];
|
|
if (!kh_exist(h, k)) continue;
|
|
x[0] = kh_key(h, k), x[1] = kh_val(h, k);
|
|
fwrite(x, 8, 2, fp);
|
|
}
|
|
}
|
|
if (!(mi->flag & MM_I_NO_SEQ))
|
|
fwrite(mi->S, 4, (sum_len + 7) / 8, fp);
|
|
fflush(fp);
|
|
}
|
|
|
|
mm_idx_t *mm_idx_load(FILE *fp)
|
|
{
|
|
char magic[4];
|
|
uint32_t x[5], i;
|
|
uint64_t sum_len = 0;
|
|
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, 5, fp) != 5) 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*)kcalloc(mi->km, mi->n_seq, sizeof(mm_idx_seq_t));
|
|
for (i = 0; i < mi->n_seq; ++i) {
|
|
uint8_t l;
|
|
mm_idx_seq_t *s = &mi->seq[i];
|
|
fread(&l, 1, 1, fp);
|
|
if (l) {
|
|
s->name = (char*)kmalloc(mi->km, l + 1);
|
|
fread(s->name, 1, l, fp);
|
|
s->name[l] = 0;
|
|
}
|
|
fread(&s->len, 4, 1, fp);
|
|
s->offset = sum_len;
|
|
sum_len += s->len;
|
|
}
|
|
for (i = 0; i < 1<<mi->b; ++i) {
|
|
mm_idx_bucket_t *b = &mi->B[i];
|
|
uint32_t j, size;
|
|
khint_t k;
|
|
idxhash_t *h;
|
|
fread(&b->n, 4, 1, fp);
|
|
b->p = (uint64_t*)malloc(b->n * 8);
|
|
fread(b->p, 8, b->n, fp);
|
|
fread(&size, 4, 1, fp);
|
|
if (size == 0) continue;
|
|
b->h = h = kh_init(idx);
|
|
kh_resize(idx, h, size);
|
|
for (j = 0; j < size; ++j) {
|
|
uint64_t x[2];
|
|
int absent;
|
|
fread(x, 8, 2, fp);
|
|
k = kh_put(idx, h, x[0], &absent);
|
|
assert(absent);
|
|
kh_val(h, k) = x[1];
|
|
}
|
|
}
|
|
if (!(mi->flag & MM_I_NO_SEQ)) {
|
|
mi->S = (uint32_t*)malloc((sum_len + 7) / 8 * 4);
|
|
fread(mi->S, 4, (sum_len + 7) / 8, fp);
|
|
}
|
|
return mi;
|
|
}
|
|
|
|
int64_t mm_idx_is_idx(const char *fn)
|
|
{
|
|
int fd, is_idx = 0;
|
|
off_t ret, off_end;
|
|
char magic[4];
|
|
|
|
if (strcmp(fn, "-") == 0) return 0; // read from pipe; not an index
|
|
fd = open(fn, O_RDONLY);
|
|
if (fd < 0) return -1; // error
|
|
if ((off_end = lseek(fd, 0, SEEK_END)) >= 4) {
|
|
lseek(fd, 0, SEEK_SET);
|
|
ret = read(fd, magic, 4);
|
|
if (ret == 4 && strncmp(magic, MM_IDX_MAGIC, 4) == 0)
|
|
is_idx = 1;
|
|
}
|
|
close(fd);
|
|
return is_idx? off_end : 0;
|
|
}
|
|
|
|
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out)
|
|
{
|
|
int64_t 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;
|
|
if (opt) r->opt = *opt;
|
|
else mm_idxopt_init(&r->opt);
|
|
if (r->is_idx) {
|
|
r->fp.idx = fopen(fn, "rb");
|
|
r->idx_size = is_idx;
|
|
} else r->fp.seq = mm_bseq_open(fn);
|
|
if (fn_out) r->fp_out = fopen(fn_out, "wb");
|
|
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);
|
|
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)
|
|
{
|
|
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->flag&MM_I_HPC) != (r->opt.flag&MM_I_HPC)))
|
|
fprintf(stderr, "[WARNING]\033[1;31m Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index.\033[0m\n");
|
|
} else
|
|
mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size);
|
|
if (mi) {
|
|
if (r->fp_out) mm_idx_dump(r->fp_out, mi);
|
|
++r->n_parts;
|
|
}
|
|
return mi;
|
|
}
|
|
|
|
int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases, mm_bseq_eof() might not work
|
|
{
|
|
return r->is_idx? (feof(r->fp.idx) || ftell(r->fp.idx) == r->idx_size) : mm_bseq_eof(r->fp.seq);
|
|
}
|