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Copy pathindex.c
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753 lines (701 loc) · 20.3 KB
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#include <stdlib.h>
#include <assert.h>
#if defined(WIN32) || defined(_WIN32)
#include <io.h> // for open(2)
#else
#include <unistd.h>
#endif
#include <fcntl.h>
#include <stdio.h>
#define __STDC_LIMIT_MACROS
#include "kthread.h"
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "kvec.h"
#include "khash.h"
#define idx_hash(a) ((a)>>1)
#define idx_eq(a, b) ((a)>>1 == (b)>>1)
KHASH_INIT(idx, uint64_t, uint64_t, 1, idx_hash, idx_eq)
typedef khash_t(idx) idxhash_t;
KHASH_MAP_INIT_STR(str, uint32_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;
typedef struct {
int32_t st, en, max; // max is not used for now
int32_t score:30, strand:2;
} mm_idx_intv1_t;
typedef struct mm_idx_intv_s {
int32_t n, m;
mm_idx_intv1_t *a;
} mm_idx_intv_t;
mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
{
mm_idx_t *mi;
if (k*2 < b) b = k * 2;
if (w < 1) w = 1;
mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t));
mi->w = w, mi->k = k, mi->b = b, mi->flag = flag;
mi->B = (mm_idx_bucket_t*)calloc(1<<b, sizeof(mm_idx_bucket_t));
if (!(mm_dbg_flag & 1)) mi->km = km_init();
return mi;
}
void mm_idx_destroy(mm_idx_t *mi)
{
uint32_t i;
if (mi == 0) return;
if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
if (mi->B) {
for (i = 0; i < 1U<<mi->b; ++i) {
free(mi->B[i].p);
free(mi->B[i].a.a);
kh_destroy(idx, (idxhash_t*)mi->B[i].h);
}
}
if (mi->I) {
for (i = 0; i < mi->n_seq; ++i)
free(mi->I[i].a);
free(mi->I);
}
if (!mi->km) {
for (i = 0; i < mi->n_seq; ++i)
free(mi->seq[i].name);
free(mi->seq);
} else km_destroy(mi->km);
free(mi->B); free(mi->S); free(mi);
}
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
{
int mask = (1<<mi->b) - 1;
khint_t k;
mm_idx_bucket_t *b = &mi->B[minier&mask];
idxhash_t *h = (idxhash_t*)b->h;
*n = 0;
if (h == 0) return 0;
k = kh_get(idx, h, minier>>mi->b<<1);
if (k == kh_end(h)) return 0;
if (kh_key(h, k)&1) { // special casing when there is only one k-mer
*n = 1;
return &kh_val(h, k);
} else {
*n = (uint32_t)kh_val(h, k);
return &b->p[kh_val(h, k)>>32];
}
}
void mm_idx_stat(const mm_idx_t *mi)
{
int n = 0, n1 = 0;
uint32_t i;
uint64_t sum = 0, len = 0;
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);
for (i = 0; i < mi->n_seq; ++i)
len += mi->seq[i].len;
for (i = 0; i < 1U<<mi->b; ++i)
if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
for (i = 0; i < 1U<<mi->b; ++i) {
idxhash_t *h = (idxhash_t*)mi->B[i].h;
khint_t k;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k)) {
sum += kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
if (kh_key(h, k)&1) ++n1;
}
}
fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf; total length: %ld\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum, (long)len);
}
int mm_idx_index_name(mm_idx_t *mi)
{
khash_t(str) *h;
uint32_t i;
int has_dup = 0, absent;
if (mi->h) return 0;
h = kh_init(str);
for (i = 0; i < mi->n_seq; ++i) {
khint_t k;
k = kh_put(str, h, mi->seq[i].name, &absent);
if (absent) kh_val(h, k) = i;
else has_dup = 1;
}
mi->h = h;
if (has_dup && mm_verbose >= 2)
fprintf(stderr, "[WARNING] some database sequences have identical sequence names\n");
return has_dup;
}
int mm_idx_name2id(const mm_idx_t *mi, const char *name)
{
khash_t(str) *h = (khash_t(str)*)mi->h;
khint_t k;
if (h == 0) return -2;
k = kh_get(str, h, name);
return k == kh_end(h)? -1 : kh_val(h, k);
}
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
{
uint64_t i, st1, en1;
if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
if (en > mi->seq[rid].len) en = mi->seq[rid].len;
st1 = mi->seq[rid].offset + st;
en1 = mi->seq[rid].offset + en;
for (i = st1; i < en1; ++i)
seq[i - st1] = mm_seq4_get(mi->S, i);
return en - st;
}
int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
{
int i;
size_t n = 0;
uint32_t thres;
khint_t *a, k;
if (f <= 0.) return INT32_MAX;
for (i = 0; i < 1<<mi->b; ++i)
if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
a = (uint32_t*)malloc(n * 4);
for (i = n = 0; i < 1<<mi->b; ++i) {
idxhash_t *h = (idxhash_t*)mi->B[i].h;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k) {
if (!kh_exist(h, k)) continue;
a[n++] = kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
}
}
thres = ks_ksmall_uint32_t(n, a, (uint32_t)((1. - f) * n)) + 1;
free(a);
return thres;
}
/*********************************
* Sort and generate hash tables *
*********************************/
static void worker_post(void *g, long i, int tid)
{
int n, n_keys;
size_t j, start_a, start_p;
idxhash_t *h;
mm_idx_t *mi = (mm_idx_t*)g;
mm_idx_bucket_t *b = &mi->B[i];
if (b->a.n == 0) return;
// sort by minimizer
radix_sort_128x(b->a.a, b->a.a + b->a.n);
// count and preallocate
for (j = 1, n = 1, n_keys = 0, b->n = 0; j <= b->a.n; ++j) {
if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
++n_keys;
if (n > 1) b->n += n;
n = 1;
} else ++n;
}
h = kh_init(idx);
kh_resize(idx, h, n_keys);
b->p = (uint64_t*)calloc(b->n, 8);
// create the hash table
for (j = 1, n = 1, start_a = start_p = 0; j <= b->a.n; ++j) {
if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
khint_t itr;
int absent;
mm128_t *p = &b->a.a[j-1];
itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
assert(absent && j == start_a + n);
if (n == 1) {
kh_key(h, itr) |= 1;
kh_val(h, itr) = p->y;
} else {
int k;
for (k = 0; k < n; ++k)
b->p[start_p + k] = b->a.a[start_a + k].y;
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
kh_val(h, itr) = (uint64_t)start_p<<32 | n;
start_p += n;
}
start_a = j, n = 1;
} else ++n;
}
b->h = h;
assert(b->n == (int32_t)start_p);
// deallocate and clear b->a
kfree(0, b->a.a);
b->a.n = b->a.m = 0, b->a.a = 0;
}
static void mm_idx_post(mm_idx_t *mi, int n_threads)
{
kt_for(n_threads, worker_post, mi, 1<<mi->b);
}
/******************
* Generate index *
******************/
#include <string.h>
#include <zlib.h>
#include "bseq.h"
typedef struct {
int mini_batch_size;
uint64_t batch_size, sum_len;
mm_bseq_file_t *fp;
mm_idx_t *mi;
} pipeline_t;
typedef struct {
int n_seq;
mm_bseq1_t *seq;
mm128_v a;
} step_t;
static void mm_idx_add(mm_idx_t *mi, int n, const mm128_t *a)
{
int i, mask = (1<<mi->b) - 1;
for (i = 0; i < n; ++i) {
mm128_v *p = &mi->B[a[i].x>>8&mask].a;
kv_push(mm128_t, 0, *p, a[i]);
}
}
static void *worker_pipeline(void *shared, int step, void *in)
{
int i;
pipeline_t *p = (pipeline_t*)shared;
if (step == 0) { // step 0: read sequences
step_t *s;
if (p->sum_len > p->batch_size) return 0;
s = (step_t*)calloc(1, sizeof(step_t));
s->seq = mm_bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
if (s->seq) {
uint32_t old_m, m;
assert((uint64_t)p->mi->n_seq + s->n_seq <= UINT32_MAX); // to prevent integer overflow
// make room for p->mi->seq
old_m = p->mi->n_seq, m = p->mi->n_seq + s->n_seq;
kroundup32(m); kroundup32(old_m);
if (old_m != m)
p->mi->seq = (mm_idx_seq_t*)krealloc(p->mi->km, p->mi->seq, m * sizeof(mm_idx_seq_t));
// make room for p->mi->S
if (!(p->mi->flag & MM_I_NO_SEQ)) {
uint64_t sum_len, old_max_len, max_len;
for (i = 0, sum_len = 0; i < s->n_seq; ++i) sum_len += s->seq[i].l_seq;
old_max_len = (p->sum_len + 7) / 8;
max_len = (p->sum_len + sum_len + 7) / 8;
kroundup64(old_max_len); kroundup64(max_len);
if (old_max_len != max_len) {
p->mi->S = (uint32_t*)realloc(p->mi->S, max_len * 4);
memset(&p->mi->S[old_max_len], 0, 4 * (max_len - old_max_len));
}
}
// populate p->mi->seq
for (i = 0; i < s->n_seq; ++i) {
mm_idx_seq_t *seq = &p->mi->seq[p->mi->n_seq];
uint32_t j;
if (!(p->mi->flag & MM_I_NO_NAME)) {
seq->name = (char*)kmalloc(p->mi->km, strlen(s->seq[i].name) + 1);
strcpy(seq->name, s->seq[i].name);
} else seq->name = 0;
seq->len = s->seq[i].l_seq;
seq->offset = p->sum_len;
seq->is_alt = 0;
// copy the sequence
if (!(p->mi->flag & MM_I_NO_SEQ)) {
for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
uint64_t o = p->sum_len + j;
int c = seq_nt4_table[(uint8_t)s->seq[i].seq[j]];
mm_seq4_set(p->mi->S, o, c);
}
}
// update p->sum_len and p->mi->n_seq
p->sum_len += seq->len;
s->seq[i].rid = p->mi->n_seq++;
}
return s;
} else free(s);
} else if (step == 1) { // step 1: compute sketch
step_t *s = (step_t*)in;
for (i = 0; i < s->n_seq; ++i) {
mm_bseq1_t *t = &s->seq[i];
if (t->l_seq > 0)
mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->flag&MM_I_HPC, &s->a);
else if (mm_verbose >= 2)
fprintf(stderr, "[WARNING] the length database sequence '%s' is 0\n", t->name);
free(t->seq); free(t->name);
}
free(s->seq); s->seq = 0;
return s;
} else if (step == 2) { // dispatch sketch to buckets
step_t *s = (step_t*)in;
mm_idx_add(p->mi, s->a.n, s->a.a);
kfree(0, s->a.a); free(s);
}
return 0;
}
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)
{
pipeline_t pl;
if (fp == 0 || mm_bseq_eof(fp)) return 0;
memset(&pl, 0, sizeof(pipeline_t));
pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
pl.batch_size = batch_size;
pl.fp = fp;
pl.mi = mm_idx_init(w, k, b, flag);
kt_pipeline(n_threads < 3? n_threads : 3, worker_pipeline, &pl, 3);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] collected minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
mm_idx_post(pl.mi, n_threads);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] sorted minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
return pl.mi;
}
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads) // a simpler interface; deprecated
{
mm_bseq_file_t *fp;
mm_idx_t *mi;
fp = mm_bseq_open(fn);
if (fp == 0) return 0;
mi = mm_idx_gen(fp, w, k, 14, flag, 1<<18, n_threads, UINT64_MAX);
mm_bseq_close(fp);
return mi;
}
mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const char **seq, const ch
8000
ar **name)
{
uint64_t sum_len = 0;
mm128_v a = {0,0,0};
mm_idx_t *mi;
khash_t(str) *h;
int i, flag = 0;
if (n <= 0) return 0;
for (i = 0; i < n; ++i) // get the total length
sum_len += strlen(seq[i]);
if (is_hpc) flag |= MM_I_HPC;
if (name == 0) flag |= MM_I_NO_NAME;
if (bucket_bits < 0) bucket_bits = 14;
mi = mm_idx_init(w, k, bucket_bits, flag);
mi->n_seq = n;
mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, n, sizeof(mm_idx_seq_t)); // ->seq is allocated from km
mi->S = (uint32_t*)calloc((sum_len + 7) / 8, 4);
mi->h = h = kh_init(str);
for (i = 0, sum_len = 0; i < n; ++i) {
const char *s = seq[i];
mm_idx_seq_t *p = &mi->seq[i];
uint32_t j;
if (name && name[i]) {
int absent;
p->name = (char*)kmalloc(mi->km, strlen(name[i]) + 1);
strcpy(p->name, name[i]);
kh_put(str, h, p->name, &absent);
assert(absent);
}
p->offset = sum_len;
p->len = strlen(s);
p->is_alt = 0;
for (j = 0; j < p->len; ++j) {
int c = seq_nt4_table[(uint8_t)s[j]];
uint64_t o = sum_len + j;
mm_seq4_set(mi->S, o, c);
}
sum_len += p->len;
if (p->len > 0) {
a.n = 0;
mm_sketch(0, s, p->len, w, k, i, is_hpc, &a);
mm_idx_add(mi, a.n, a.a);
}
}
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;
s->is_alt = 0;
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;
int64_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
#ifdef WIN32
if ((off_end = _lseeki64(fd, 0, SEEK_END)) >= 4) {
_lseeki64(fd, 0, SEEK_SET);
#else
if ((off_end = lseek(fd, 0, SEEK_END)) >= 4) {
lseek(fd, 0, SEEK_SET);
#endif // WIN32
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);
mi->index = 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);
}
#include <ctype.h>
#include <zlib.h>
#include "ksort.h"
#include "kseq.h"
KSTREAM_DECLARE(gzFile, gzread)
int mm_idx_alt_read(mm_idx_t *mi, const char *fn)
{
int n_alt = 0;
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) return -1;
ks = ks_init(fp);
if (mi->h == 0) mm_idx_index_name(mi);
while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
char *p;
int id;
for (p = str.s; *p && !isspace(*p); ++p) { }
*p = 0;
id = mm_idx_name2id(mi, str.s);
if (id >= 0) mi->seq[id].is_alt = 1, ++n_alt;
}
mi->n_alt = n_alt;
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s] found %d ALT contigs\n", __func__, n_alt);
return n_alt;
}
#define sort_key_bed(a) ((a).st)
KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)
mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn, int read_junc)
{
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
mm_idx_intv_t *I;
fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) return 0;
I = (mm_idx_intv_t*)calloc(mi->n_seq, sizeof(*I));
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
mm_idx_intv_t *r;
mm_idx_intv1_t t = {-1,-1,-1,-1,0};
char *p, *q, *bl, *bs;
int32_t i, id = -1, n_blk = 0;
for (p = q = str.s, i = 0;; ++p) {
if (*p == 0 || *p == '\t') {
int32_t c = *p;
*p = 0;
if (i == 0) { // chr
id = mm_idx_name2id(mi, q);
if (id < 0) break; // unknown name; TODO: throw a warning
} else if (i == 1) { // start
t.st = atol(q); // TODO: watch out integer overflow!
if (t.st < 0) break;
} else if (i == 2) { // end
t.en = atol(q);
if (t.en < 0) break;
} else if (i == 4) { // BED score
t.score = atol(q);
} else if (i == 5) { // strand
t.strand = *q == '+'? 1 : *q == '-'? -1 : 0;
} else if (i == 9) {
if (!isdigit(*q)) break;
n_blk = atol(q);
} else if (i == 10) {
bl = q;
} else if (i == 11) {
bs = q;
break;
}
if (c == 0) break;
++i, q = p + 1;
}
}
if (id < 0 || t.st < 0 || t.st >= t.en) continue;
r = &I[id];
if (i >= 11 && read_junc) { // BED12
int32_t st, sz, en;
st = strtol(bs, &bs, 10); ++bs;
sz = strtol(bl, &bl, 10); ++bl;
en = t.st + st + sz;
for (i = 1; i < n_blk; ++i) {
mm_idx_intv1_t s = t;
if (r->n == r->m) {
r->m = r->m? r->m + (r->m>>1) : 16;
r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
}
st = strtol(bs, &bs, 10); ++bs;
sz = strtol(bl, &bl, 10); ++bl;
s.st = en, s.en = t.st + st;
en = t.st + st + sz;
if (s.en > s.st) r->a[r->n++] = s;
}
} else {
if (r->n == r->m) {
r->m = r->m? r->m + (r->m>>1) : 16;
r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
}
r->a[r->n++] = t;
}
}
free(str.s);
ks_destroy(ks);
gzclose(fp);
return I;
}
int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
{
int32_t i;
if (mi->h == 0) mm_idx_index_name(mi);
mi->I = mm_idx_read_bed(mi, fn, read_junc);
if (mi->I == 0) return -1;
for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals
radix_sort_bed(mi->I[i].a, mi->I[i].a + mi->I[i].n);
return 0;
}
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s)
{
int32_t i, left, right;
mm_idx_intv_t *r;
memset(s, 0, en - st);
if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1;
r = &mi->I[ctg];
left = 0, right = r->n;
while (right > left) {
int32_t mid = left + ((right - left) >> 1);
if (r->a[mid].st >= st) right = mid;
else left = mid + 1;
}
for (i = left; i < r->n; ++i) {
if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0) {
if (r->a[i].strand > 0) {
s[r->a[i].st - st] |= 1, s[r->a[i].en - 1 - st] |= 2;
} else {
s[r->a[i].st - st] |= 8, s[r->a[i].en - 1 - st] |= 4;
}
}
}
return left;
}