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wtsky.c
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/*
*
* Copyright (c) 2011, Jue Ruan <[email protected]>
*
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "list.h"
#include "hashset.h"
#include "dna.h"
#include "kswx.h"
#include "hzm_aln.h"
#include "file_reader.h"
#include "bitvec.h"
#include "thread.h"
#include <getopt.h>
#define HZMH_KMER_MOD 1024
#define hzmh_kmer_smear(K) ((K) ^ ((K) >> 4) ^ ((K) >> 7) ^ ((K) >> 12))
#define HZM_MAX_SEED_KMER 32
typedef struct {
uint32_t rd_id:31, dir:1;
} hzmin_t;
define_list(hzminv, hzmin_t);
typedef struct {
hzm_t p1;
hzmin_t *p2;
uint64_t beg, end;
} hz_ref_t;
define_list(hzrefv, hz_ref_t);
#define tmp_util1(r) (((r)->p2->rd_id << 1) | (r)->p2->dir)
#define heap_cmp_hz_ref_macro(refs, a, b) \
({ \
hz_ref_t *r1, *r2; \
r1 = ref_hzrefv(refs, a); \
r2 = ref_hzrefv(refs, b); \
(tmp_util1(r1) > tmp_util1(r2))? 1 : ((tmp_util1(r1) < tmp_util1(r2))? -1 : ((r1->p1.off > r2->p1.off)? 1 : ((r1->p1.off < r2->p1.off)? -1 : 0))); \
})
#define WTZMO_SR_SEED_MAX_OVL ((1U<<20)-1)
#define WTZMO_SR_SEED_MAX_CNT ((1U<<12)-1)
typedef struct {
uint32_t pb1:31, dir1:1;
uint32_t pb2:30, dir2:1, closed:1;
uint32_t ovl:20, cnt:12;
uint32_t anchors[2];
int beg[2];
int end[2];
int avg, std, pseudo_ovl;
} sr_seed_t;
static const sr_seed_t SR_SEED_NULL = (sr_seed_t){0, 0, 0, 0, 0, 0, 0, {0, 0}, {0, 0}, {0, 0}, 0, 0, 0};
define_list(srseedv, sr_seed_t);
#define srseed_hashcode(E) (((E).pb2 << 1) | (E).dir2)
#define srseed_hashequals(E1, E2) ((E1).pb2 == (E2).pb2 && (E1).dir2 == (E2).dir2)
define_hashset(srseedhash, sr_seed_t, srseed_hashcode, srseed_hashequals);
typedef struct {
uint32_t pb1:31, dir1:1, pb2:31, dir2:1;
int qb, qe, tb, te;
int score, mat, mis, ins, del, aln;
char *cigar;
} wt_ovl_t;
define_list(wtovlv, wt_ovl_t);
#define _ovl_uniq_long_id(id1, id2, dir) ((((uint64_t)(id1)) << 33) | (((uint64_t)(id2)) << 1) | (dir))
#define ovl_uniq_long_id(id1, id2, dir) (((id1) < (id2))? _ovl_uniq_long_id(id1, id2, dir) : _ovl_uniq_long_id(id2, id1, dir))
typedef struct {
uint64_t rdoff:40, rdlen:24;
char *rdname;
} pbread_t;
define_list(pbreadv, pbread_t);
typedef struct {
uint64_t link:62, closed:1, dir:1;
} wtlink_t;
typedef struct {
uint32_t nodes[2];
wtlink_t links[2];
} wtedge_t;
typedef struct {
uint64_t seqoff:40, seqlen:23, closed:1;
struct { uint64_t bt_visit:19, bt_dir:1, bt_idx:10, bt_off:34; };
wtlink_t edges[2];
} wtnode_t;
typedef struct {
uint32_t n_rd;
BaseBank *rdseqs;
pbreadv *reads;
cuhash *rdname2id;
vplist *rdhits;
hzminv *seeds;
hzmhash *hashs[HZMH_KMER_MOD];
BitVec *masked;
BitVec *needed;
u64hash *closed_alns;
u32list *rdcovs;
int hk, hz;
uint32_t ksize, zsize, n_idx, kwin, kstep, kovl, ksave, ztot, zovl, max_kmer_freq, max_zmer_freq, max_kmer_var, win_rep_cutoff;
uint32_t ncand, nbest;
int w, ew, W, M, X, O, E, T;
int8_t matrix[4*4];
int off_esti;
int min_score;
float min_id;
uint32_t max_unalign_in_contained;
uint32_t max_unalign_in_dovetail;
float skip_contained;
int best_overlap;
int debug;
} WTZMO;
WTZMO* init_wtzmo(uint32_t ksize, uint32_t zsize, int w, int W, int M, int X, int O, int E, int T, int min_score, float min_id){
WTZMO *wt;
int i;
wt = malloc(sizeof(WTZMO));
wt->rdseqs = init_basebank();
wt->reads = init_pbreadv(1024);
wt->rdname2id = init_cuhash(1023);
wt->seeds = init_hzminv(1024);
for(i=0;i<HZMH_KMER_MOD;i++){
wt->hashs[i] = init_hzmhash(1023);
}
wt->masked = init_bitvec(1024);
wt->needed = init_bitvec(1024);
wt->closed_alns = init_u64hash(1023);
wt->rdcovs = init_u32list(1024);
wt->rdhits = init_vplist(1024);
wt->n_rd = 0;
wt->n_idx = 1;
wt->ksize = ksize;
wt->zsize = zsize;
wt->kwin = 500;
wt->kstep = 0;
wt->kovl = 200;
wt->ksave = 0;
wt->ztot = 200;
wt->zovl = 100;
wt->win_rep_cutoff = 100;
wt->max_kmer_freq = 10000;
wt->max_zmer_freq = 100;
wt->max_kmer_var = 5;
wt->w = w;
wt->W = W;
wt->ew = (w + W) / 2;
wt->M = M;
wt->X = X;
wt->O = O;
wt->E = E;
wt->T = T;
for(i=0;i<4*4;i++) wt->matrix[i] = ((i % 4) == (i / 4))? M : X;
wt->off_esti = 1;
wt->skip_contained = 1;
wt->min_score = min_score;
wt->min_id = min_id;
wt->ncand = 1000;
wt->nbest = 50;
wt->max_unalign_in_contained = 0;
wt->max_unalign_in_dovetail = 200;
wt->best_overlap = 0;
wt->debug = 0;
return wt;
}
void free_wtzmo(WTZMO *wt){
uint32_t i;
free_basebank(wt->rdseqs);
for(i=0;i<wt->n_rd;i++) free(wt->reads->buffer[i].rdname);
free_pbreadv(wt->reads);
free_cuhash(wt->rdname2id);
free_u64hash(wt->closed_alns);
free_bitvec(wt->masked);
free_bitvec(wt->needed);
free_u32list(wt->rdcovs);
for(i=0;i<wt->rdhits->size;i++) free_u64list((u64list*)get_vplist(wt->rdhits, i));
free_vplist(wt->rdhits);
for(i=0;i<HZMH_KMER_MOD;i++){
free_hzmhash(wt->hashs[i]);
}
free_hzminv(wt->seeds);
free(wt);
}
void push_long_read_wtzmo(WTZMO *wt, char *name, int name_len, char *seq, int seq_len){
char *ptr;
ptr = malloc(name_len + 1);
memcpy(ptr, name, name_len);
ptr[name_len] = 0;
push_pbreadv(wt->reads, (pbread_t){wt->rdseqs->size, seq_len, ptr});
seq2basebank(wt->rdseqs, seq, seq_len);
wt->n_rd ++;
}
void set_read_clip_wtzmo(WTZMO *wt, char *name, int coff, int clen){
pbread_t *rd;
uint32_t pbid;
if((pbid = kv_get_cuhash(wt->rdname2id, name)) == 0xFFFFFFFFU) return;
rd = ref_pbreadv(wt->reads, pbid);
if(coff < 0 || coff + clen > (int)rd->rdlen) return;
rd->rdoff += coff;
rd->rdlen = clen;
}
thread_beg_def(midx);
WTZMO *wt;
uint32_t beg, end;
int task;
thread_end_def(midx);
thread_beg_func(midx);
WTZMO *wt;
hzmh_t *u, U;
pbread_t *rd;
uint64_t kmer, krev, kmask, off, kidx;
uint32_t beg, end, pbid, pblen, i, j, ncpu, tidx;
uint8_t b, c, dir;
int exists;
wt = midx->wt;
beg = midx->beg;
end = midx->end;
ncpu = midx->n_cpu;
tidx = midx->t_idx;
kmask = 0xFFFFFFFFFFFFFFFFLLU >> ((32 - wt->ksize) << 1);
memset(&U, 0, sizeof(hzmh_t));
thread_beg_loop(midx);
if(midx->task == 1){
for(pbid=beg;pbid<end;pbid++){
if(tidx == 0 && ((pbid - beg) % 1000) == 0){ fprintf(stderr, "\r%u", pbid - beg); fflush(stderr); }
rd = ref_pbreadv(wt->reads, pbid);
pblen = rd->rdlen;
b = 4;
kmer = 0;
off = rd->rdoff;
for(i=j=0;j<pblen;j++){
c = bits2bit(wt->rdseqs->bits, off); off ++;
if(wt->hk && c == b) continue;
b = c;
i ++;
kmer = ((kmer << 2) | b) & kmask;
if(i < wt->ksize) continue;
krev = dna_rev_seq(kmer, wt->ksize);
if(krev == kmer) continue;
dir = krev > kmer? 0 : 1;
krev = krev > kmer? kmer : krev;
if(wt->ksave && (krev & 0x03) > 1) continue; // skip G and T
kidx = hzmh_kmer_smear(krev) % HZMH_KMER_MOD;
if((kidx % ncpu) != tidx) continue;
U.mer = krev;
u = prepare_hzmhash(wt->hashs[kidx], U, &exists);
if(exists){
if(u->cnt < 0xFFFFU) u->cnt ++;
} else {
u->mer = krev;
u->off = 0;
u->cnt = 1;
u->flt = 0;
}
}
}
if(tidx == 0) fprintf(stderr, "\r%u reads\n", end - beg); fflush(stderr);
} else if(midx->task == 2){
for(pbid=beg;pbid<end;pbid++){
if(tidx == 0 && ((pbid - beg) % 1000) == 0){ fprintf(stderr, "\r%u", pbid - beg); fflush(stderr); }
rd = ref_pbreadv(wt->reads, pbid);
pblen = rd->rdlen;
b = 4;
kmer = 0;
off = rd->rdoff;
for(i=j=0;j<pblen;j++){
c = bits2bit(wt->rdseqs->bits, off); off ++;
if(wt->hk && c == b) continue;
b = c;
i ++;
kmer = ((kmer << 2) | b) & kmask;
if(i < wt->ksize) continue;
krev = dna_rev_seq(kmer, wt->ksize);
if(krev == kmer) continue;
dir = krev > kmer? 0 : 1;
krev = krev > kmer? kmer : krev;
if(wt->ksave && (krev & 0x03) > 1) continue; // skip G and T
kidx = hzmh_kmer_smear(krev) % HZMH_KMER_MOD;
if((kidx % ncpu) != tidx) continue;
U.mer = krev;
u = get_hzmhash(wt->hashs[kidx], U);
if(u == NULL || u->flt || u->cnt >= wt->max_kmer_freq) continue; // too high or singleton
wt->seeds->buffer[u->off + u->cnt] = (hzmin_t){pbid, dir};
u->cnt ++;
}
}
if(tidx == 0) fprintf(stderr, "\r%u reads\n", pbid - beg); fflush(stderr);
}
thread_end_loop(midx);
thread_end_func(midx);
void index_wtzmo(WTZMO *wt, uint32_t beg, uint32_t end, uint32_t ncpu){
hzmh_t *u;
uint64_t nflt, nrem, none, ktot, off;
uint32_t ktyp, kavg, i;
thread_preprocess(midx);
clear_hzminv(wt->seeds);
for(i=0;i<HZMH_KMER_MOD;i++){
clear_hzmhash(wt->hashs[i]);
}
thread_beg_init(midx, ncpu);
midx->wt = wt;
midx->beg = beg;
midx->end = end;
midx->task = 0;
thread_end_init(midx);
fprintf(stderr, "[%s] - scanning kmers (%d bp)\n", date(), wt->ksize);
thread_apply_all(midx, midx->task = 1); // finish task1
// estimate kmer_freq_cutoff
if(wt->max_kmer_freq < 2){
ktot = ktyp = 0;
for(i=0;i<HZMH_KMER_MOD;i++){
reset_iter_hzmhash(wt->hashs[i]);
while((u = ref_iter_hzmhash(wt->hashs[i]))){
ktot += u->cnt;
}
ktyp += wt->hashs[i]->count;
}
kavg = ktot / (ktyp + 1);
if(kavg < 20) kavg = 20;
wt->max_kmer_freq = kavg * 5;
fprintf(stderr, "[%s] - high frequency kmer depth is set to %d\n", date(), wt->max_kmer_freq);
}
ktot = nrem = none = nflt = ktyp = 0;
off = 0;
for(i=0;i<HZMH_KMER_MOD;i++){
reset_iter_hzmhash(wt->hashs[i]);
while((u = ref_iter_hzmhash(wt->hashs[i]))){
ktot += u->cnt;
if(u->cnt > wt->max_kmer_freq){ u->cnt = wt->max_kmer_freq; nflt ++; }
{
u->off = off;
off += u->cnt;
u->cnt = 0;
nrem ++;
}
}
ktyp += wt->hashs[i]->count;
}
clear_and_encap_hzminv(wt->seeds, off);
wt->seeds->size = off;
kavg = ktot / (ktyp + 1);
fprintf(stderr, "[%s] - average kmer depth = %d\n", date(), kavg);
//fprintf(stderr, "[%s] - %llu single kmers (==1)\n", date(), (unsigned long long)none);
fprintf(stderr, "[%s] - %llu high frequency kmers (>=%d)\n", date(), (unsigned long long)nflt, wt->max_kmer_freq);
fprintf(stderr, "[%s] - indexing %llu kmers\n", date(), (unsigned long long)nrem);
thread_apply_all(midx, midx->task = 2); // finish task2
thread_beg_close(midx);
thread_end_close(midx);
}
void query_wtzmo(WTZMO *wt, uint32_t pbid, u64list *candidates, hzrefv *refs, u32list *heap, u32list *hzoff){
hz_ref_t *r, R;
pbread_t *rd;
hzmh_t *h;
hzm_t *p1, P1;
hzmin_t *p2, P2;
uint64_t kmer, krev, kmask, off, x1, x2;
uint32_t i, j, pblen, ol, lst, kidx, id1, id2, cnt, dir;
uint8_t b, c;
kmask = 0xFFFFFFFFFFFFFFFFLLU >> ((32 - wt->ksize) << 1);
rd = ref_pbreadv(wt->reads, pbid);
pblen = rd->rdlen;
R.p1 = (hzm_t){0xFFFFFFFFU, 0, 0, 0};
P2 = (hzmin_t){0x7FFFFFFFU, 0};
R.p2 = &P2;
R.beg = R.end = 0;
p1 = &P1;
b = 4;
kmer = 0;
clear_hzrefv(refs);
clear_u32list(heap);
clear_u32list(hzoff);
off = rd->rdoff;
for(i=j=0;j<pblen;j++){
c = bits2bit(wt->rdseqs->bits, off); off ++;
if(wt->hk && c == b) continue;
b = c;
i ++;
push_u32list(hzoff, j);
kmer = ((kmer << 2) | b) & kmask;
if(i < wt->ksize) continue;
krev = dna_rev_seq(kmer, wt->ksize);
if(krev == kmer) continue;
p1->dir = krev > kmer? 0 : 1;
krev = krev > kmer? kmer : krev;
if(wt->ksave && (krev & 0x03) > 1) continue; // skip G and T
kidx = hzmh_kmer_smear(krev) % HZMH_KMER_MOD;
h = get_hzmhash(wt->hashs[kidx], (hzmh_t){krev, 0, 0, 0});
if(h == NULL) continue;
if(wt->debug > 3){
fprintf(stdout, "KMER\t%u\t%u\t%u\n", hzoff->buffer[i - wt->ksize], i - wt->ksize, h? h->cnt : 0);
}
if(h->flt) continue;
p1->mer = krev;
p1->off = hzoff->buffer[i - wt->ksize];
p1->len = (j + 1 - p1->off > HZM_MAX_SEED_LEN)? HZM_MAX_SEED_LEN : j + 1 - p1->off;
r = next_ref_hzrefv(refs);
r->p1 = P1;
r->beg = h->off;
r->end = h->off + h->cnt;
while(r->beg < r->end){
r->p2 = ref_hzminv(wt->seeds, r->beg ++);
if(r->p2->rd_id == pbid) continue;
if(wt->reads->buffer[r->p2->rd_id].rdlen > pblen) continue;
array_heap_push(heap->buffer, heap->size, heap->cap, uint32_t, refs->size - 1, heap_cmp_hz_ref_macro(refs, a, b));
break;
}
}
id2 = 0xFFFFFFFFU;
ol = 0;
lst = 0;
cnt = 0;
dir = 0;
x1 = x2 = 0xFFFFFFFF00000000LLU;
while(1){
id1 = array_heap_pop(heap->buffer, heap->size, heap->cap, uint32_t, heap_cmp_hz_ref_macro(refs, a, b));
if(id1 != 0xFFFFFFFFU){
r = ref_hzrefv(refs, id1);
} else r = &R;
p1 = &r->p1;
p2 = r->p2;
if(id2 != p2->rd_id || dir != p2->dir){
if(id2 != 0xFFFFFFFFU){
if(ol >= wt->kovl){
x2 = (((uint64_t)id2) << 32) | ol;
if(((x1 >> 32) == (x2 >> 32))){ x1 = (x1 & 0xFFFFFFFFU) > (x2 & 0xFFFFFFFFU)? x1 : x2;}
else if(x1 == 0xFFFFFFFF00000000LLU){ x1 = x2; }
else {
if(candidates->size >= wt->ncand) array_heap_remove(candidates->buffer, candidates->size, candidates->cap, uint64_t, 0,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
array_heap_push(candidates->buffer, candidates->size, candidates->cap, uint64_t, x1,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
x1 = x2;
}
}
if(wt->debug > 2){
fprintf(stdout, "FAXIAN\t%s\t%d\t%d\t%c\n", wt->reads->buffer[id2].rdname, ol, cnt, "+-"[dir]);
}
}
id2 = p2->rd_id;
dir = p2->dir;
ol = 0;
lst = 0;
cnt = 0;
}
if(id1 == 0xFFFFFFFFU) break;
if(p1->off >= lst) ol += p1->len;
else ol += p1->off + p1->len - lst;
lst = p1->off + p1->len;
cnt ++;
while(r->beg < r->end){
r->p2 = ref_hzminv(wt->seeds, r->beg ++);
if(r->p2->rd_id == pbid) continue;
if(wt->reads->buffer[r->p2->rd_id].rdlen > pblen) continue;
array_heap_push(heap->buffer, heap->size, heap->cap, uint32_t, id1, heap_cmp_hz_ref_macro(refs, a, b));
break;
}
}
if(x1 != 0xFFFFFFFF00000000LLU){
if(candidates->size >= wt->ncand) array_heap_remove(candidates->buffer, candidates->size, candidates->cap, uint64_t, 0,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
array_heap_push(candidates->buffer, candidates->size, candidates->cap, uint64_t, x1,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
}
}
thread_beg_def(mzmo);
WTZMO *wt;
uint32_t rd_id, bcov;
int do_align, fast_align, just_query;
wtovlv *hits;
wtseedv *seeds, *windows;
u32list *masks;
thread_end_def(mzmo);
thread_beg_func(mzmo);
WTZMO *wt;
hzrefv *refs;
hzmhv *zhash;
hzmv *zseeds;
BitVec *zbits;
wtseedv *seeds, *windows, *windows2;
wt_seed_t *seed, SEED[2];
wt_seed_t *zp;
hzmpv *cache, *anchors, *anchors2;
wtovlv *hits;
u32hash *masked;
String *cigar_str;
wt_ovl_t HIT, *hit;
kswx_t x;
u32list *heap;
u64list *candidates;
u16list *windeps;
u32list *hzoff;
alnregv *regs;
aln_reg_t REG;
u8list *rdseq, *hzseq, *pb1, *pb2;
u8list *mem_pbseq, *mem_cache[2];
u32list *mem_cigar, *cigar_cache, *cigars;
uint64_t val, *u;
uint32_t i, j, k, dir, id2, x1, x2, x3, x4, ol, pbid, avg, *ptr, bcov, ncand;
int alen, blen, exists;
wt = mzmo->wt;
hits = mzmo->hits;
masked = init_u32hash(1023);
seeds = mzmo->seeds;
windows = mzmo->windows;
windows2 = init_wtseedv(1024);
cache = init_hzmpv(1024);
anchors = init_hzmpv(1024);
anchors2 = init_hzmpv(1024);
hit = &HIT;
pb1 = init_u8list(1024);
pb2 = init_u8list(1024);
cigar_str = init_string(1024);
rdseq = init_u8list(1024);
hzseq = init_u8list(1024);
hzoff = init_u32list(1024);
heap = init_u32list(1024);
refs = init_hzrefv(1024);
zhash = init_hzmhv(1023);
zseeds = init_hzmv(1024);
mem_pbseq = init_u8list(1024);
mem_cache[0] = init_u8list(1024);
mem_cache[1] = init_u8list(1024);
cigars = init_u32list(1024);
mem_cigar = init_u32list(1024);
cigar_cache = init_u32list(1024);
memset(&SEED[0], 0, sizeof(wt_seed_t));
memset(&SEED[1], 0, sizeof(wt_seed_t));
regs = init_alnregv(1024);
thread_beg_loop(mzmo);
pbid = mzmo->rd_id;
alen = wt->reads->buffer[pbid].rdlen;
if(wt->rdhits->size) candidates = (u64list*)get_vplist(wt->rdhits, pbid);
else candidates = init_u64list(1024);
query_wtzmo(wt, pbid, candidates, refs, heap, hzoff);
if(mzmo->just_query) continue;
sort_array(candidates->buffer, candidates->size, uint64_t, (b & 0xFFFFFFFFU) > (a & 0xFFFFFFFFU));
if(wt->debug){
fprintf(stdout, "=%s\n", wt->reads->buffer[pbid].rdname);
for(i=0;i<candidates->size;i++){
id2 = get_u64list(candidates, i) >> 32;
fprintf(stdout, "CANDIDATE\t%s\t%d\n", wt->reads->buffer[id2].rdname, (uint32_t)get_u64list(candidates, i));
}
fprintf(stdout, "Total candidates: %u\n", (unsigned)candidates->size);
}
clear_wtseedv(seeds);
clear_wtseedv(windows);
clear_wtovlv(hits);
clear_hzmpv(cache);
clear_hzmpv(anchors);
windeps = init_u16list(wt->reads->buffer[pbid].rdlen);
zeros_u16list(windeps);
zbits = init_bitvec(0xFFFFFFFFFFFFFFFFLLU >> ((32 - wt->zsize) << 1));
clear_and_encap_u8list(pb1, alen);
bitseq_basebank(wt->rdseqs, wt->reads->buffer[pbid].rdoff, alen, pb1->buffer);
index_single_read_seeds(pb1->buffer, alen, wt->zsize, wt->hz, 64, zhash, zbits, zseeds, hzoff);
for(i=0;i<candidates->size;i++){
id2 = get_u64list(candidates, i) >> 32;
clear_hzmpv(cache);
blen = wt->reads->buffer[id2].rdlen;
clear_and_encap_u8list(pb2, blen);
bitseq_basebank(wt->rdseqs, wt->reads->buffer[id2].rdoff, blen, pb2->buffer);
query_single_read_seeds(pb2->buffer, blen, wt->zsize, wt->hz, wt->max_kmer_var, zhash, zbits, zseeds, hzoff, cache);
if(wt->debug > 2){
fprintf(stdout, "Query\t%s\t%d\n", wt->reads->buffer[id2].rdname, (int)cache->size);
}
if(cache->size * wt->zsize < wt->ztot) continue;
process_hzmps(cache, wt->reads->buffer[id2].rdlen);
for(dir=0;dir<2;dir++){
//SEED[dir].pb1 = pbid;
SEED[dir].pb2 = id2;
SEED[dir].dir = dir;
SEED[dir].ovl = 0;
SEED[dir].closed = 1;
clear_wtseedv(windows2);
clear_hzmpv(anchors2);
if(merge_paired_kmers_window(cache, dir, windows2, anchors2, mem_cache, wt->zsize, wt->kwin, wt->kstep, wt->zovl) == 0) continue;
SEED[dir].ovl = chaining_wtseedv(pbid, id2, dir, windows2, 0, windows2->size, mem_cache[0], wt->W);
if(SEED[dir].ovl < wt->ztot) continue;
SEED[dir].anchors[0] = windows->size;
for(j=0;j<windows2->size;j++){
zp = ref_wtseedv(windows2, j);
if(zp->closed) continue;
append_array_hzmpv(anchors, anchors2->buffer + zp->anchors[0], zp->anchors[1] - zp->anchors[0]);
zp->anchors[1] = zp->anchors[1] - zp->anchors[0];
zp->anchors[0] = anchors->size - zp->anchors[1];
zp->anchors[1] = anchors->size;
push_wtseedv(windows, *zp);
for(k=zp->beg[0];(int)k<zp->end[0];k++) windeps->buffer[k] ++;
}
SEED[dir].anchors[1] = windows->size;
SEED[dir].closed = 0;
}
dir = (SEED[0].ovl < SEED[1].ovl);
if(SEED[dir].ovl >= wt->ztot) push_wtseedv(seeds, SEED[dir]);
}
free_bitvec(zbits);
if(wt->rdhits->size == 0) free_u64list(candidates);
if(wt->debug){
fprintf(stdout, "TOTAL SEEDS: %u\n", (uint32_t)seeds->size);
}
// Filter repeat-matching only seeds
if(wt->debug > 3){
for(i=0;(int)i<alen;i++){
fprintf(stdout, "REP[%d]\t%d\t%c\n", i, windeps->buffer[i], windeps->buffer[i] >= wt->win_rep_cutoff? 'R' : 'U');
}
}
if(wt->skip_contained) clear_u32hash(masked);
ncand = 0;
for(i=0;i<seeds->size;i++){
seed = ref_wtseedv(seeds, i);
if(seed->closed) continue;
ol = 0;
for(j=seed->anchors[0];j<seed->anchors[1];j++){
zp = ref_wtseedv(windows, j);
if(zp->closed) continue;
avg = 0;
for(k=zp->beg[0];(int)k<zp->end[0];k++) avg += windeps->buffer[k];
avg = avg / (zp->end[0] - zp->beg[0] + 1);
if(wt->debug > 1){
fprintf(stdout, "WINREP\t%s\t%d\t%d\t%d\t%d\t%d\n", wt->reads->buffer[seed->pb2].rdname, zp->beg[0], zp->end[0], zp->beg[1], zp->end[1], avg);
}
if(avg < wt->win_rep_cutoff){ ol += zp->end[0] - zp->beg[0] + 1; }
}
if(ol < wt->ztot){
seed->closed = 1; ncand ++;
if(wt->debug){
fprintf(stdout, "Filter %s, non-repetitive seed size %d\n", wt->reads->buffer[seed->pb2].rdname, ol);
}
} else if(wt->debug > 1){
fprintf(stdout, "Keep %s, non-repetitive seed size %d\n", wt->reads->buffer[seed->pb2].rdname, ol);
}
}
free_u16list(windeps);
if(wt->debug){
fprintf(stdout, "Filtered %u repetitive-seq-caused seeds\n", ncand);
}
sort_array(seeds->buffer, seeds->size, wt_seed_t, b.ovl > a.ovl);
thread_beg_syn(mzmo);
for(i=0;i<seeds->size;i++){
seed = ref_wtseedv(seeds, i);
if(seed->closed) continue;
//val = ovl_uniq_long_id(seed->pb2, seed->pb1, seed->dir);
val = ovl_uniq_long_id(seed->pb2, pbid, seed->dir);
u = prepare_u64hash(wt->closed_alns, val, &exists);
if(!exists) *u = val;
else seed->closed = 2;
}
thread_end_syn(mzmo);
//sort_array(seeds->buffer, seeds->size, wt_seed_t, b.ovl > a.ovl);
//sort_array(seeds->buffer, seeds->size, wt_seed_t, (a.closed > b.closed)? 1 : ((a.closed == b.closed)? (b.ovl > a.ovl) : 0));
//for(i=0;i<seeds->size;i++) if(seeds->buffer[i].closed == 2){ seeds->size = i; break; }
if(mzmo->do_align){
bcov = mzmo->bcov;
ncand = wt->ncand;
for(i=0;i<seeds->size&&i<ncand;i++){
seed = ref_wtseedv(seeds, i);
if(seed->closed){ ncand ++; continue; }
blen = wt->reads->buffer[seed->pb2].rdlen;
clear_and_encap_u8list(pb2, blen);
if(seed->dir) revbitseq_basebank(wt->rdseqs, wt->reads->buffer[seed->pb2].rdoff, blen, pb2->buffer);
else bitseq_basebank(wt->rdseqs, wt->reads->buffer[seed->pb2].rdoff, blen, pb2->buffer);
if(wt->debug){
fprintf(stdout, "DO_ALIGN\t%04d\t%s\t%s\t%c\t%d\n", i, wt->reads->buffer[pbid].rdname, wt->reads->buffer[seed->pb2].rdname, "+-"[seed->dir], seed->ovl);
}
clear_u32list(cigar_cache);
clear_alnregv(regs);
for(j=seed->anchors[0];j<seed->anchors[1];j++){
zp = ref_wtseedv(windows, j);
if(zp->closed) continue;
REG.cigar_off = cigar_cache->size;
REG.x = fast_seeds_align_hzmo(pb1->buffer, pb2->buffer, zp, anchors, cigar_cache, mem_cache[0], mem_cigar, wt->w, wt->M, wt->X, wt->O, wt->O, wt->E, wt->T);
REG.cigar_len = cigar_cache->size - REG.cigar_off;
if(REG.x.aln * 2 < (int)wt->zovl || REG.x.mat < REG.x.aln * wt->min_id) continue;
push_alnregv(regs, REG);
}
if(regs->size == 0){ seed->closed = 1; ncand ++; continue; }
x = global_align_regs_hzmo(alen, blen, regs, (int[2]){0, alen}, (uint8_t*[2]){pb1->buffer, pb2->buffer}, cigar_cache->buffer, cigars, mem_cache[0], mem_cigar, wt->W, wt->ew, wt->w, wt->M, wt->X, wt->O, wt->O, wt->E, wt->T);
clear_alnregv(regs);
if(wt->debug){
fprintf(stdout, "OVL\t%s\t%c\t%d\t%d\t%d\t%s\t%c\t%d\t%d\t%d", wt->reads->buffer[pbid].rdname, '+', alen, x.tb, x.te, wt->reads->buffer[seed->pb2].rdname, "+-"[seed->dir], blen, x.qb, x.qe);
fprintf(stdout, "\t%d\t%0.3f\t%d\t%d\t%d\t%d\n", x.score, 1.0 * x.mat / x.aln, x.mat, x.mis, x.ins, x.del);
}
if(x.score < wt->min_score || x.mat < x.aln * wt->min_id) continue;
clear_string(cigar_str);
kswx_cigar2string(cigar_str, cigars->size, cigars->buffer);
//HIT.pb1 = seed->pb1;
HIT.pb1 = pbid;
HIT.pb2 = seed->pb2;
HIT.dir1 = 0;
HIT.dir2 = seed->dir;
HIT.score = x.score;
HIT.tb = x.tb;
HIT.te = x.te;
HIT.qb = x.qb;
HIT.qe = x.qe;
HIT.mat = x.mat;
HIT.mis = x.mis;
HIT.ins = x.ins;
HIT.del = x.del;
HIT.aln = x.aln;
HIT.cigar = strdup(cigar_str->string);
push_wtovlv(mzmo->hits, HIT);
{
x1 = num_min(hit->tb, hit->qb);
x2 = num_min(((int)wt->reads->buffer[hit->pb1].rdlen) - hit->te, ((int)wt->reads->buffer[hit->pb2].rdlen) - hit->qe);
if(x1 + x2 <= wt->max_unalign_in_dovetail){
if(wt->skip_contained){
hit = &HIT;
x3 = ((hit->tb == 0 && hit->qb) || (hit->te == (int)wt->reads->buffer[hit->pb1].rdlen && hit->qe < (int)wt->reads->buffer[hit->pb2].rdlen));
x4 = ((hit->qb == 0 && hit->tb) || (hit->qe == (int)wt->reads->buffer[hit->pb2].rdlen && hit->te < (int)wt->reads->buffer[hit->pb1].rdlen));
x1 = wt->reads->buffer[hit->pb2].rdlen + hit->qb - hit->qe;
x2 = wt->reads->buffer[hit->pb1].rdlen + hit->tb - hit->te;
if(x1 <= wt->max_unalign_in_contained && x3 == 0){
if(x2 <= wt->max_unalign_in_contained && x4 == 0){
if(wt->reads->buffer[hit->pb1].rdlen > wt->reads->buffer[hit->pb2].rdlen){
put_u32hash(masked, hit->pb2);
} else if(wt->reads->buffer[hit->pb1].rdlen < wt->reads->buffer[hit->pb2].rdlen){
put_u32hash(masked, hit->pb1); break;
} else if(hit->pb2 > hit->pb1){
put_u32hash(masked, hit->pb2); continue;
} else {
put_u32hash(masked, hit->pb1); break;
}
} else {
put_u32hash(masked, hit->pb2); continue;
}
ncand ++;
} else if(x2 <= wt->max_unalign_in_contained && x4 == 0){
put_u32hash(masked, hit->pb1); break;
ncand ++;
}
}
x1 = num_max(0, HIT.tb);
x2 = num_min((int)wt->kwin, HIT.te);
if(x1 < x2) bcov += x2 - x1;
x3 = num_max(alen - (int)wt->kwin, HIT.tb);
x4 = num_min(alen, HIT.te);
if(x3 < x4) bcov += x4 - x3;
if(wt->debug){
fprintf(stdout, "COV\t%d\t%d\t%d\t%d\t%d\n", bcov, x1, x2, x3, x4);
}
if(bcov >= 2 * wt->kwin * wt->nbest){
if(wt->debug){
fprintf(stdout, "COVBREAK\t%d\t%d\n", bcov, 2 * wt->kwin * wt->nbest);
}
break;
}
}
}
}
//wt->rdcovs->buffer[pbid] = bcov; // thread-unsafe
mzmo->bcov = bcov; // thread-unsafe
}
//else if(1){ seeds->size = 0; }
if(wt->skip_contained){
reset_iter_u32hash(masked);
while((ptr = ref_iter_u32hash(masked))){
push_u32list(mzmo->masks, *ptr);
}
}
thread_end_loop(mzmo);
free_u8list(rdseq);
free_u8list(hzseq);
free_u32list(hzoff);
free_string(cigar_str);
free_u8list(pb1);
free_u8list(pb2);
free_u32hash(masked);
free_wtseedv(windows2);
free_hzmpv(anchors);
free_hzmpv(anchors2);
free_hzmpv(cache);
free_u32list(heap);
free_hzrefv(refs);
free_hzmhv(zhash);
free_hzmv(zseeds);
free_u8list(mem_pbseq);
free_u8list(mem_cache[0]);
free_u8list(mem_cache[1]);
free_u32list(cigars);
free_u32list(mem_cigar);
free_u32list(cigar_cache);
free_alnregv(regs);
thread_end_func(mzmo);
//uint32_t print_hits_wtzmo(WTZMO *wt, wtseedv *seeds, wtovlv *hits, FILE *out){
uint32_t print_hits_wtzmo(WTZMO *wt, uint32_t pbid, wtseedv *seeds, wtovlv *hits, FILE *out){
wt_ovl_t *hit;
wt_seed_t *seed;
uint32_t i, j, ret, x1, x2;
ret = 0;
if(seeds){
for(i=j=0;i<seeds->size;i++){
seed = ref_wtseedv(seeds, i);
if(seed->closed) continue;
fprintf(out, "# %s\t%c\t%d", wt->reads->buffer[pbid].rdname, "+-"[0], wt->reads->buffer[pbid].rdlen);
fprintf(out, "\t%s\t%c\t%d", wt->reads->buffer[seed->pb2].rdname, "+-"[seed->dir], wt->reads->buffer[seed->pb2].rdlen);
fprintf(out, "\t%d\n", seed->ovl);
if(j == hits->size) continue;
hit = ref_wtovlv(hits, j);
if(hit->score == -19830203){ if(hit->cigar){ free(hit->cigar); hit->cigar = NULL; } j ++; continue; }
if(hit->pb2 != seed->pb2) continue;
j ++;
ret ++;
if(hit->aln == 0) hit->aln = 1;
x1 = num_min(hit->tb, hit->qb);
x2 = num_min(((int)wt->reads->buffer[hit->pb1].rdlen) - hit->te, ((int)wt->reads->buffer[hit->pb2].rdlen) - hit->qe);
if(x1 + x2 <= wt->max_unalign_in_dovetail){
x1 = num_max(0, hit->qb);
x2 = num_min((int)wt->kwin, hit->qe);
if(x1 < x2) wt->rdcovs->buffer[hit->pb2] += x2 - x1;
x1 = num_max(((int)(wt->reads->buffer[hit->pb2].rdlen)) - ((int)wt->kwin), hit->qb);
x2 = num_min(((int)(wt->reads->buffer[hit->pb2].rdlen)), hit->qe);
if(x1 < x2) wt->rdcovs->buffer[hit->pb2] += x2 - x1;
}
fprintf(out, "%s\t%c\t%d\t%d\t%d", wt->reads->buffer[hit->pb1].rdname, "+-"[hit->dir1], wt->reads->buffer[hit->pb1].rdlen, hit->tb, hit->te);
fprintf(out, "\t%s\t%c\t%d\t%d\t%d", wt->reads->buffer[hit->pb2].rdname, "+-"[hit->dir2], wt->reads->buffer[hit->pb2].rdlen, hit->qb, hit->qe);
fprintf(out, "\t%d\t%0.3f\t%d\t%d\t%d\t%d", hit->score, 1.0 * hit->mat / hit->aln, hit->mat, hit->mis, hit->ins, hit->del);
if(hit->cigar){
fprintf(out, "\t%s\n", hit->cigar);
free(hit->cigar);
hit->cigar = NULL;
} else {
fprintf(out, "\t0M\n");
}
}
clear_wtseedv(seeds);
} else {
for(j=0;j<hits->size;j++){
hit = ref_wtovlv(hits, j);
if(hit->score == -19830203){ if(hit->cigar){ free(hit->cigar); hit->cigar = NULL; } j ++; continue; }
ret ++;
if(hit->aln == 0) hit->aln = 1;
x1 = num_min(hit->tb, hit->qb);
x2 = num_min(((int)wt->reads->buffer[hit->pb1].rdlen) - hit->te, ((int)wt->reads->buffer[hit->pb2].rdlen) - hit->qe);
if(x1 + x2 <= wt->max_unalign_in_dovetail){
x1 = num_max(0, hit->qb);
x2 = num_min((int)wt->kwin, hit->qe);
if(x1 < x2) wt->rdcovs->buffer[hit->pb2] += x2 - x1;
x1 = num_max(((int)(wt->reads->buffer[hit->pb2].rdlen)) - ((int)wt->kwin), hit->qb);
x2 = num_min(((int)(wt->reads->buffer[hit->pb2].rdlen)), hit->qe);
if(x1 < x2) wt->rdcovs->buffer[hit->pb2] += x2 - x1;
}
fprintf(out, "%s\t%c\t%d\t%d\t%d", wt->reads->buffer[hit->pb1].rdname, "+-"[hit->dir1], wt->reads->buffer[hit->pb1].rdlen, hit->tb, hit->te);
fprintf(out, "\t%s\t%c\t%d\t%d\t%d", wt->reads->buffer[hit->pb2].rdname, "+-"[hit->dir2], wt->reads->buffer[hit->pb2].rdlen, hit->qb, hit->qe);
fprintf(out, "\t%d\t%0.3f\t%d\t%d\t%d\t%d", hit->score, 1.0 * hit->mat / hit->aln, hit->mat, hit->mis, hit->ins, hit->del);
if(hit->cigar){
fprintf(out, "\t%s\n", hit->cigar);
free(hit->cigar);
hit->cigar = NULL;
} else {
fprintf(out, "\t0M\n");
}
}
}
clear_wtovlv(hits);
return ret;
}
uint64_t overlap_wtzmo(WTZMO *wt, int ncpu, int do_align, int fast_align, uint32_t n_job, uint32_t i_job, FILE *out){
uint64_t ret;
uint32_t i, j, rd_id, pbbeg, pbend, i_idx;
int n_cpu;
thread_preprocess(mzmo);
if(wt->debug) n_cpu = 1;
else n_cpu = ncpu;
thread_beg_init(mzmo, n_cpu);
mzmo->wt = wt;
mzmo->rd_id = 0xFFFFFFFFU;
mzmo->bcov = 0;
mzmo->do_align = do_align;
mzmo->fast_align = fast_align;
mzmo->just_query = 0;
mzmo->seeds = init_wtseedv(1024);
mzmo->windows = init_wtseedv(1024);
mzmo->hits = init_wtovlv(1024);
mzmo->masks = init_u32list(16);
thread_end_init(mzmo);
ret = 0;
if(wt->n_idx > 1){
for(j=0;j<wt->n_rd;j++) push_vplist(wt->rdhits, init_u64list(2));
}
pbbeg = pbend = 0;
for(i_idx=0;i_idx<wt->n_idx;i_idx++){
pbbeg = pbend;
pbend = pbbeg + (wt->n_rd + wt->n_idx - 1) / wt->n_idx;
fprintf(stderr, "[%s] indexing %u/%u\n", date(), i_idx + 1, wt->n_idx);
index_wtzmo(wt, pbbeg, pbend, ncpu);
fprintf(stderr, "[%s] Done\n", date());
fprintf(stderr, "[%s] querying %u/%u\n", date(), i_idx + 1, wt->n_idx);
if(i_idx + 1 >= wt->n_idx) break;
for(j=0;j<wt->n_rd;j++){
rd_id = j;
if((rd_id % n_job) != i_job) continue;
if(get_bitvec(wt->masked, rd_id)) continue;
thread_waitfor_one_idle(mzmo);
mzmo->just_query = 1;
mzmo->rd_id = rd_id;
thread_wake(mzmo);
if((j % 100) == 0){
fprintf(stderr, "\r%u", j); fflush(stderr);
}
}
thread_waitfor_all_idle(mzmo);
fprintf(stderr, "\rprogress: %u 100.00%%\n", wt->n_rd); fflush(stderr);
}
for(j=0;j<wt->n_rd;j++){
rd_id = j;
if((rd_id % n_job) != i_job) continue;
if(get_bitvec(wt->masked, rd_id)) continue;
thread_waitfor_one_idle(mzmo);
mzmo->just_query = 0;
if(mzmo->rd_id != 0xFFFFFFFFU) wt->rdcovs->buffer[mzmo->rd_id] = mzmo->bcov;
ret += print_hits_wtzmo(wt, mzmo->rd_id, do_align? NULL : mzmo->seeds, mzmo->hits, out);
if(wt->skip_contained){
thread_beg_syn_write(mzmo);
for(i=0;i<mzmo->masks->size;i++) one_bitvec(wt->masked, mzmo->masks->buffer[i]);
thread_end_syn_write(mzmo);
}
clear_u32list(mzmo->masks);
mzmo->rd_id = rd_id;
mzmo->bcov = wt->rdcovs->buffer[rd_id];
//mzmo->bcov = 0;
thread_wake(mzmo);
if((j % 100) == 0){
fprintf(stderr, "\r%012u\t%llu", j, (unsigned long long)ret); fflush(stderr);
}
}
thread_waitfor_all_idle(mzmo);
thread_beg_close(mzmo);
if(mzmo->rd_id != 0xFFFFFFFFU) wt->rdcovs->buffer[mzmo->rd_id] = mzmo->bcov;
ret += print_hits_wtzmo(wt, mzmo->rd_id, do_align? NULL : mzmo->seeds, mzmo->hits, out);
if(wt->skip_contained){
thread_beg_syn_write(mzmo);
for(i=0;i<mzmo->masks->size;i++) one_bitvec(wt->masked, mzmo->masks->buffer[i]);
thread_end_syn_write(mzmo);
}
free_wtovlv(mzmo->hits);
free_wtseedv(mzmo->seeds);
free_wtseedv(mzmo->windows);
free_u32list(mzmo->masks);
thread_end_close(mzmo);
fprintf(stderr, "\rprogress: %u %llu 100.00%%\n", wt->n_rd, (unsigned long long)ret); fflush(stderr);
return ret;
}
uint64_t online_overlap_wtzmo(WTZMO *wt, int ncpu, int do_align, int fast_align, uint32_t n_job, uint32_t i_job, FileReader *fr, FILE *out){
uint64_t ret;
uint32_t i, j, rd_id;
thread_preprocess(mzmo);
fprintf(stderr, "[%s] indexing whole reads in online mode\n", date());
index_wtzmo(wt, 0, wt->n_rd, ncpu);
fprintf(stderr, "[%s] Done\n", date());
if(wt->debug) ncpu = 1;
thread_beg_init(mzmo, ncpu);
mzmo->wt = wt;
mzmo->rd_id = 0xFFFFFFFFU;
mzmo->bcov = 0;
mzmo->do_align = do_align;
mzmo->fast_align = fast_align;
mzmo->just_query = 0;
mzmo->seeds = init_wtseedv(1024);
mzmo->windows = init_wtseedv(1024);
mzmo->hits = init_wtovlv(1024);
mzmo->masks = init_u32list(16);
thread_end_init(mzmo);
ret = 0;
j = 0;
while(fread_line(fr->line, fr) != -1){
if(fr->line->string[0] == '#') continue;