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wtzmo.c
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wtzmo.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 zmo_debug_out stderr
#define DO_NOTHING 0
#define HZMH_KMER_MOD 1024
//#define hzmh_kmer_smear(K) ((K) ^ ((K) >> 4) ^ ((K) >> 7) ^ ((K) >> 12))
#define hzmh_kmer_smear(K) __lh3_Jenkins_hash_int((uint32_t)K)
#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 {
uint32_t n_rd, n_qr;
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 hzmh_kmer_mod;
uint32_t ksize, zsize, n_idx, kwin, kstep, kovl, ksave, ztot, zovl, max_kmer_freq, max_zmer_freq, max_kmer_var;
float win_rep_norm, win_rep_cutoff;
uint32_t avg_rdlen;
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 dot_matrix, xvar, yvar, min_block_len, max_overhang;
float deviation_penalty, gap_penalty;
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(64);
wt->rdname2id = init_cuhash(1023);
wt->seeds = init_hzminv(64);
for(i=0;i<HZMH_KMER_MOD;i++){
wt->hashs[i] = init_hzmhash(1023);
}
wt->masked = init_bitvec(64);
wt->needed = init_bitvec(64);
wt->closed_alns = init_u64hash(1023);
wt->rdcovs = init_u32list(64);
wt->rdhits = init_vplist(64);
wt->n_rd = 0;
wt->n_qr = 0;
wt->n_idx = 1;
wt->ksave = 1;
wt->hzmh_kmer_mod = HZMH_KMER_MOD * wt->ksave;
wt->ksize = ksize;
wt->zsize = zsize;
wt->kwin = 500;
wt->kstep = 0;
wt->kovl = 200;
wt->ztot = 200;
wt->zovl = 100;
wt->win_rep_norm = 10;
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->avg_rdlen = 10000;
wt->ncand = 1000;
wt->nbest = 50;
wt->max_unalign_in_contained = 0;
wt->max_unalign_in_dovetail = 200;
wt->best_overlap = 0;
wt->dot_matrix = 0;
wt->xvar = 256;
wt->yvar = 32;
wt->min_block_len = 512;
wt->max_overhang = 256;
wt->deviation_penalty = 0.1;
wt->gap_penalty = 0.01;
wt->debug = 0;
return wt;
}
void free_wtzmo(WTZMO *wt){
uint32_t i;
free_basebank(wt->rdseqs);
for(i=0;i<wt->n_rd+wt->n_qr;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(zmo_debug_out, "\r%u", pbid - beg); fflush(zmo_debug_out); }
if(DO_NOTHING) continue;
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) % wt->hzmh_kmer_mod;
if(kidx >= HZMH_KMER_MOD) continue;
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(zmo_debug_out, "\r%u reads\n", end - beg);} fflush(zmo_debug_out);
} else if(midx->task == 2){
for(pbid=beg;pbid<end;pbid++){
if(tidx == 0 && ((pbid - beg) % 1000) == 0){ fprintf(zmo_debug_out, "\r%u", pbid - beg); fflush(zmo_debug_out); }
if(DO_NOTHING) continue;
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) % wt->hzmh_kmer_mod;
if(kidx >= HZMH_KMER_MOD) continue;
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(zmo_debug_out, "\r%u reads\n", pbid - beg);} fflush(zmo_debug_out);
}
thread_end_loop(midx);
thread_end_func(midx);
thread_beg_def(msrt);
WTZMO *wt;
thread_end_def(msrt);
thread_beg_func(msrt);
WTZMO *wt;
hzmhash *hash;
hzmh_t *e;
hzmin_t *hs;
uint32_t ncpu, tidx, i;
wt = msrt->wt;
ncpu = msrt->n_cpu;
tidx = msrt->t_idx;
thread_beg_loop(msrt);
if(DO_NOTHING) continue;
for(i=tidx;i<HZMH_KMER_MOD;i+=ncpu){
hash = wt->hashs[i];
reset_iter_hzmhash(hash);
while((e = ref_iter_hzmhash(hash))){
if(e->cnt <= 1) continue;
hs = wt->seeds->buffer + e->off;
sort_array(hs, e->cnt, hzmin_t, (a.rd_id > b.rd_id)? 1 : (a.rd_id == b.rd_id? a.dir > b.dir : 0));
}
}
thread_end_loop(msrt);
thread_end_func(msrt);
void index_wtzmo(WTZMO *wt, uint32_t beg, uint32_t end, uint32_t ncpu){
hzmh_t *u;
uint64_t nflt, nrem, none, ktot, off, totlen;
uint32_t ktyp, kavg, i;
thread_preprocess(midx);
int wushigang = midx_j;
thread_preprocess(msrt);
wushigang = msrt_j;
int tmp = wushigang;
wushigang = tmp;
totlen = 0;
if(wt->n_qr == 0 && wt->n_rd){
for(i=0;i<wt->n_rd;i++) totlen += wt->reads->buffer[i].rdlen;
wt->avg_rdlen = totlen / wt->n_rd;
} else if(wt->n_qr){
for(i=0;i<wt->n_qr;i++) totlen += wt->reads->buffer[i + wt->n_rd].rdlen;
wt->avg_rdlen = totlen / wt->n_qr;
} else wt->avg_rdlen = 10000;
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(zmo_debug_out, "[%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(zmo_debug_out, "[%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 ++; }
if(u->cnt > wt->max_kmer_freq){ u->cnt = 0; u->flt = 1; nflt ++; }
{
u->off = off;
off += u->cnt;
if(u->cnt <= 1) u->flt = 1;
else nrem ++;
u->cnt = 0;
}
}
ktyp += wt->hashs[i]->count;
}
clear_and_encap_hzminv(wt->seeds, off);
wt->seeds->size = off;
kavg = ktot / (ktyp + 1);
fprintf(zmo_debug_out, "[%s] - average kmer depth = %d\n", date(), kavg);
//fprintf(zmo_debug_out, "[%s] - %llu single kmers (==1)\n", date(), (unsigned long long)none);
fprintf(zmo_debug_out, "[%s] - %llu high frequency kmers (>=%d)\n", date(), (unsigned long long)nflt, wt->max_kmer_freq);
fprintf(zmo_debug_out, "[%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);
// sort hzmin_t by p->rd_id + p->dir, for dir is not ordered
thread_beg_init(msrt, ncpu);
msrt->wt = wt;
thread_end_init(msrt);
thread_wake_all(msrt);
thread_wait_all(msrt);
thread_beg_close(msrt);
thread_end_close(msrt);
}
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, pblen_up, ol, lst, kidx, id1, id2, cnt, dir;
uint8_t b, c, has_next;
kmask = 0xFFFFFFFFFFFFFFFFLLU >> ((32 - wt->ksize) << 1);
rd = ref_pbreadv(wt->reads, pbid);
pblen = rd->rdlen;
pblen_up = pblen * 1.2;
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;
kidx = hzmh_kmer_smear(krev) % wt->hzmh_kmer_mod;
if(kidx >= HZMH_KMER_MOD) continue;
h = get_hzmhash(wt->hashs[kidx], (hzmh_t){krev, 0, 0, 0});
if(h == NULL) continue;
if(wt->debug > 3){
fprintf(zmo_debug_out, "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_up) 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){
if(heap->size){
id1 = heap->buffer[0];
r = ref_hzrefv(refs, id1);
p1 = &r->p1;
p2 = r->p2;
has_next = 0;
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_up) continue;
array_heap_replace(heap->buffer, heap->size, heap->cap, uint32_t, 0, id1, heap_cmp_hz_ref_macro(refs, a, b));
has_next = 1;
break;
}
if(has_next == 0) array_heap_remove(heap->buffer, heap->size, heap->cap, uint32_t, 0, heap_cmp_hz_ref_macro(refs, a, b));
} else {
id1 = 0xFFFFFFFFU;
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){
if((candidates->buffer[0] & 0xFFFFFFFFU) < ol){
array_heap_replace(candidates->buffer, candidates->size, candidates->cap, uint64_t, 0, x1,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
//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));
}
} else {
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(zmo_debug_out, "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(wt->debug > 3){
fprintf(zmo_debug_out, "HEAP\t%s\t%c\t%d\t%d\n", wt->reads->buffer[id2].rdname, "+-"[dir], p1->off, p1->len);
}
if(p1->off >= lst) ol += p1->len;
else ol += p1->off + p1->len - lst;
lst = p1->off + p1->len;
cnt ++;
}
if(candidates->size >= wt->ncand){
if((candidates->buffer[0] & 0xFFFFFFFFU) < ol){
array_heap_replace(candidates->buffer, candidates->size, candidates->cap, uint64_t, 0, x1,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
}
} else {
array_heap_push(candidates->buffer, candidates->size, candidates->cap, uint64_t, x1,
((a & 0xFFFFFFFFU) > (b & 0xFFFFFFFFU))? 1 : (((a & 0xFFFFFFFFU) < (b & 0xFFFFFFFFU))? -1 : 0));
}
//if(candidates->size != 7777777) candidates->size = 0; // TODO DEBUG
}
typedef struct {
WTZMO *wt;
u32list *rdids;
u32list *alnoffs;
uint32_t rdlen;
u32list *bases[4];
BitVec *solid;
vplist *matrix;
uint32_t min_mac;
float min_freq;
} SimpMSA;
static inline SimpMSA* init_simpMSA(WTZMO *wt, float min_allele_freq, uint32_t min_allele_count){
SimpMSA *msa;
msa = malloc(sizeof(SimpMSA));
msa->wt = wt;
msa->rdlen = 0;
msa->rdids = init_u32list(64);
msa->alnoffs = init_u32list(64);
msa->bases[0] = init_u32list(64);
msa->bases[1] = init_u32list(64);
msa->bases[2] = init_u32list(64);
msa->bases[3] = init_u32list(64);
msa->solid = init_bitvec(64);
msa->matrix = init_vplist(64);
msa->min_freq = min_allele_freq;
msa->min_mac = min_allele_count;
return msa;
}
static inline void free_simpMSA(SimpMSA *msa){
uint32_t i;
free_u32list(msa->rdids);
free_u32list(msa->alnoffs);
free_u32list(msa->bases[0]);
free_u32list(msa->bases[1]);
free_u32list(msa->bases[2]);
free_u32list(msa->bases[3]);
free_bitvec(msa->solid);
for(i=0;i<msa->matrix->size;i++) free_u8list((u8list*)get_vplist(msa->matrix, i));
free_vplist(msa->matrix);
free(msa);
}
static inline void reset_simpMSA(SimpMSA *msa, uint32_t rdlen, uint32_t rdid, u8list *seq){
uint32_t i;
msa->rdlen = rdlen;
for(i=0;i<msa->matrix->size;i++) free_u8list((u8list*)get_vplist(msa->matrix, i));
clear_vplist(msa->matrix); push_u32list(msa->alnoffs, 0); push_u32list(msa->rdids, rdid); push_vplist(msa->matrix, seq);
}
static inline void push_simpMSA(SimpMSA *msa, wt_ovl_t *hit, u8list *pb2, u32list *cigar){
u8list *seq;
uint32_t i, j, x1, x2, op, len;
x1 = hit->tb;
x2 = hit->qb;
push_u32list(msa->rdids, hit->pb2);
push_u32list(msa->alnoffs, hit->tb);
seq = init_u8list(msa->rdlen);
for(i=0;i<x1;i++) push_u8list(seq, 5);
for(i=0;i<cigar->size;i++){
op = cigar->buffer[i] & 0xF;
len = cigar->buffer[i] >> 4;
switch(op){
case 0:
if(len >= 5) for(j=0;j<len;j++) push_u8list(seq, pb2->buffer[x2 + j]);
else for(j=0;j<len;j++) push_u8list(seq, 4);
x1 += len; x2 += len; break;
case 2: for(j=0;j<len;j++) push_u8list(seq, 4); x1 += len; break;
default: x2 += len;
}
}
for(i=x1;i<msa->rdlen;i++) push_u8list(seq, 5);
push_vplist(msa->matrix, seq);
}
static inline void call_simpMSA(SimpMSA *msa, FILE *out){
u8list *seq, *ref;
u32list *difs, *order, *keys;
uint32_t I, i, J, j, tot, mac;
if(msa->matrix->size < 1) return;
for(i=0;i<4;i++){
clear_and_encap_u32list(msa->bases[i], msa->rdlen);
zeros_u32list(msa->bases[i]);
}
for(i=0;i<msa->matrix->size;i++){
seq = (u8list*)get_vplist(msa->matrix, i);
for(j=0;j<msa->rdlen;j++){
if(seq->buffer[j] < 4) msa->bases[seq->buffer[j]]->buffer[j] ++;
}
}
ref = (u8list*)get_vplist(msa->matrix, 0);
clear_bitvec(msa->solid);
keys = init_u32list(32);
for(i=0;i<msa->rdlen;i++){
tot = 0;
mac = 0;
for(j=0;j<4;j++){
tot += msa->bases[j]->buffer[i];
if(j != ref->buffer[i]) mac += msa->bases[j]->buffer[i];
}
msa->bases[0]->buffer[i] = mac = num_min(tot - mac, mac);
if(mac >= msa->min_mac && mac >= tot * msa->min_freq){
one2bitvec(msa->solid);
push_u32list(keys, i);
} else zero2bitvec(msa->solid);
}
sort_array(keys->buffer, keys->size, uint32_t, msa->bases[0]->buffer[b] > msa->bases[0]->buffer[a]);
difs = init_u32list(msa->matrix->size);
for(i=0;i<msa->matrix->size;i++){
tot = 0;
seq = (u8list*)get_vplist(msa->matrix, i);
for(J=0;J<keys->size;J++){
j = keys->buffer[J];
if(seq->buffer[j] == ref->buffer[j]) tot ++;
}
push_u32list(difs, tot);
}
order = init_u32list(msa->matrix->size);
for(i=0;i<msa->matrix->size;i++) push_u32list(order, i);
sort_array(order->buffer + 1, order->size - 1, uint32_t, difs->buffer[b] > difs->buffer[a]);
for(I=0;I<msa->matrix->size;I++){
i = order->buffer[I];
fprintf(out, "MSA\t%s\t", msa->wt->reads->buffer[msa->rdids->buffer[i]].rdname);
seq = (u8list*)get_vplist(msa->matrix, i);
for(J=0;J<keys->size;J++){
j = keys->buffer[J];
fputc(seq->buffer[j] == ref->buffer[j]? '.' : "ACGT--"[seq->buffer[j]], out);
//fputc("ACGT--"[seq->buffer[j]], out);
}
fprintf(out, "\n");
}
free_u32list(order);
free_u32list(keys);
free_u32list(difs);
}
thread_beg_def(mzmo);
WTZMO *wt;
uint32_t rd_id, bcov;
int do_align, fast_align, just_query, refine;
wtovlv *hits;
wtseedv *seeds, *windows;
u32list *masks;
u64list *closed;
thread_end_def(mzmo);
thread_beg_func(mzmo);
WTZMO *wt;
hzrefv *refs;
hzmhv *zhash;
hzmv *zseeds;
BitVec *zbits;
wtseedv *seeds, *windows, *windows2, *wins[2];
wt_seed_t *seed, SEED[2];
wt_seed_t *zp;
hzmpv *cache, *anchors, *anchors2, *dst[2];
diagv *diags;
wtovlv *hits;
u32hash *masked;
String *cigar_str;
wt_ovl_t HIT, *hit;
kswx_t x;
u32list *heap;
u64list *candidates;
u16list *windeps;
f4v *weights;
u32list *hzoff;
alnregv *regs;
aln_reg_t REG;
u4v *block, *grps;
u8list *rdseq, *hzseq, *pb1, *pb2;
u8list *mem_pbseq, *mem_cache[2];
u32list *mem_cigar, *cigar_cache, *cigars;
u1v * kcnts;
SimpMSA *msa;
u8list *mseq;
kswr_t r;
uint64_t val;
uint32_t i, j, k, dir, id2, x1, x2, x3, x4, ol, pbid, *ptr, bcov, ncand, nbest;
bcov = 0;
uint32_t wushigang = bcov;
uint32_t tmp = wushigang;
wushigang = tmp;
double avg;
int alen, blen;
wt = mzmo->wt;
hits = mzmo->hits;
masked = init_u32hash(1023);
seeds = mzmo->seeds;
windows = mzmo->windows;
windows2 = init_wtseedv(64);
cache = init_hzmpv(64);
anchors = init_hzmpv(64);
anchors2 = init_hzmpv(64);
hit = &HIT;
pb1 = init_u8list(64);
pb2 = init_u8list(64);
cigar_str = init_string(64);
rdseq = init_u8list(64);
hzseq = init_u8list(64);
hzoff = init_u32list(64);
heap = init_u32list(64);
refs = init_hzrefv(64);
zhash = init_hzmhv(1023);
zseeds = init_hzmv(64);
windeps = init_u16list(64);
weights = init_f4v(64);
mem_pbseq = init_u8list(64);
mem_cache[0] = init_u8list(64);
mem_cache[1] = init_u8list(64);
cigars = init_u32list(64);
mem_cigar = init_u32list(64);
cigar_cache = init_u32list(64);
memset(&SEED[0], 0, sizeof(wt_seed_t));
memset(&SEED[1], 0, sizeof(wt_seed_t));
kcnts = init_u1v(1024);
regs = init_alnregv(64);
msa = init_simpMSA(wt, 0.20, 4);
//for dot matrix alignment
dst[0] = init_hzmpv(64);
dst[1] = init_hzmpv(64);
wins[0] = init_wtseedv(64);
wins[1] = init_wtseedv(64);
diags = init_diagv(64);
block = init_u4v(64);
grps = init_u4v(64);
thread_beg_loop(mzmo);
if(DO_NOTHING) continue;
pbid = mzmo->rd_id;
nbest = ((size_t)wt->nbest) * wt->reads->buffer[pbid].rdlen / wt->avg_rdlen;
if(nbest < wt->nbest) nbest = wt->nbest;
if(mzmo->bcov >= nbest) break;
alen = wt->reads->buffer[pbid].rdlen;
if(wt->rdhits->size) candidates = (u64list*)get_vplist(wt->rdhits, pbid);
else candidates = init_u64list(64);
query_wtzmo(wt, pbid, candidates, refs, heap, hzoff);
thread_beg_syn_read(mzmo);
for(i=0;i<candidates->size;i++){
id2 = get_u64list(candidates, i) >> 32;
if(exists_u64hash(wt->closed_alns, ovl_uniq_long_id(pbid, id2, 0))){
candidates->buffer[i] &= 0xFFFFFFFF00000000LLU;
}
}
thread_end_syn_read(mzmo);
sort_array(candidates->buffer, candidates->size, uint64_t, (b & 0xFFFFFFFFU) > (a & 0xFFFFFFFFU));
while(candidates->size && (candidates->buffer[candidates->size - 1] & 0xFFFFFFFFU) == 0){ candidates->size --; }
if(wt->debug){
fprintf(zmo_debug_out, "=%s\n", wt->reads->buffer[pbid].rdname);
for(i=0;i<candidates->size;i++){
id2 = get_u64list(candidates, i) >> 32;
fprintf(zmo_debug_out, "CANDIDATE\t%s\t%d\n", wt->reads->buffer[id2].rdname, (uint32_t)get_u64list(candidates, i));
}
fprintf(zmo_debug_out, "Total candidates: %u\n", (unsigned)candidates->size);
}
if(mzmo->just_query) continue;
clear_wtseedv(seeds);
clear_wtseedv(windows);
clear_wtovlv(hits);
clear_hzmpv(cache);
clear_hzmpv(anchors);
encap_u16list(windeps, wt->reads->buffer[pbid].rdlen);
memset(windeps->buffer, 0, wt->reads->buffer[pbid].rdlen * sizeof(uint16_t));
encap_f4v(weights, wt->reads->buffer[pbid].rdlen);
//windeps = init_u16list(wt->reads->buffer[pbid].rdlen);
//weights = init_f4v(wt->reads->buffer[pbid].rdlen);
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, wt->max_zmer_freq, zhash, zbits, zseeds, hzoff);
for(i=0;i<candidates->size;i++){
id2 = get_u64list(candidates, i) >> 32;
//if(exists_u64hash(wt->closed_alns, ovl_uniq_long_id(pbid, id2, 0))) continue;
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_zmer_freq, wt->max_kmer_var, zhash, zbits, zseeds, hzoff, kcnts, cache);
if(wt->debug > 2){
fprintf(zmo_debug_out, "Query\t%s\t%d\n", wt->reads->buffer[id2].rdname, (int)cache->size);
}
if(cache->size * wt->zsize < wt->ztot) continue;
if(wt->dot_matrix){
val = ovl_uniq_long_id(id2, pbid, 0);
push_u64list(mzmo->closed, val);
r = dot_matrix_align_hzmps(cache, dst, wins, diags, block, grps, mem_cache[0], alen, blen, wt->xvar, wt->yvar, wt->min_block_len, wt->max_overhang, wt->deviation_penalty, wt->gap_penalty);
ol = num_max(r.qe - r.qb, r.te - r.tb);
if(r.score >= wt->min_score && r.score >= (int)(wt->min_id * ol)){
HIT.pb1 = pbid;
HIT.pb2 = id2;
HIT.dir1 = 0;
HIT.dir2 = r.score2;
HIT.score = r.score;
HIT.tb = r.tb;
HIT.te = r.te;
HIT.qb = r.qb;
HIT.qe = r.qe;
HIT.mat = r.score;
HIT.mis = 0;
HIT.ins = 0;
HIT.del = 0;
HIT.aln = ol;
HIT.cigar = NULL;
push_wtovlv(mzmo->hits, HIT);
}
if(wt->reads->size == 2 && hzm_debug){
// generate dot_plot.fwd.src.txt, dot_plot.fwd.dst.txt, dot_plot.rev.src.txt, dot_plot.rev.dst.txt
debug_dot_plot_hzmps(cache);
}
continue;
}
process_hzmps(cache);
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->dot_matrix){
// dot matrix mode, already finish alignment into mzmo->hits
continue;
}
if(wt->debug){
fprintf(zmo_debug_out, "TOTAL SEEDS: %u\n", (uint32_t)seeds->size);
}
/*
if(wt->win_rep_cutoff != (int)wt->win_rep_cutoff){
for(i=val=0;i<wt->reads->buffer[pbid].rdlen;i++) val += windeps->buffer[i];
avg = (val + wt->reads->buffer[pbid].rdlen - 1)/ wt->reads->buffer[pbid].rdlen;
if(avg < 20) avg = 20;
rep_cutoff = avg * wt->win_rep_cutoff;
} else rep_cutoff = wt->win_rep_cutoff;
*/
for(i=0;(int)i<alen;i++)
weights->buffer[i] = (windeps->buffer[i] <= wt->win_rep_norm)? 1.0
: ((windeps->buffer[i] >= wt->win_rep_cutoff)? 0.0 : wt->win_rep_norm / (float)windeps->buffer[i]);
for(i=0;(int)i<alen;i++) weights->buffer[i] = weights->buffer[i] * (0.3 + 0.7 * (num_diff(((int)i), alen / 2) / (alen / 2.0)));
if(wt->debug > 3){
for(i=0;(int)i<alen;i++){
fprintf(zmo_debug_out, "REP[%d]\t%d\t%0.3f\n", i, windeps->buffer[i], weights->buffer[i]);
}
}
if(wt->skip_contained) clear_u32hash(masked);
ncand = 0;
for(i=0;i<seeds->size;i++){
seed = ref_wtseedv(seeds, i);
blen = wt->reads->buffer[seed->pb2].rdlen;
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 += weights->buffer[k];
avg = (zp->end[0] - zp->beg[0]) * weights->buffer[(zp->beg[0] + zp->end[0]) / 2];
// Consider the position of candidate
avg = avg * (0.3 + 0.7 * (num_diff(((int)((zp->beg[1] + zp->end[1]) / 2)), blen / 2) / (blen / 2.0)));
if(wt->debug > 1){
fprintf(zmo_debug_out, "WINREP\t%s\t%d\t%d\t%d\t%d\t%0.3f\n", wt->reads->buffer[seed->pb2].rdname, zp->beg[0], zp->end[0], zp->beg[1], zp->end[1], avg);
}
ol += avg;
//if(avg < rep_cutoff){ ol += zp->end[0] - zp->beg[0] + 1; }
}
seed->ovl = ol;
if(ol * wt->win_rep_cutoff < wt->ztot * wt->win_rep_norm){
seed->closed = 1; ncand ++;
if(wt->debug){
fprintf(zmo_debug_out, "Filter %s, non-repetitive seed size %d\n", wt->reads->buffer[seed->pb2].rdname, ol);
}
}
/*
if(ol < wt->ztot){
seed->closed = 1; ncand ++;
if(wt->debug){
fprintf(zmo_debug_out, "Filter %s, non-repetitive seed size %d\n", wt->reads->buffer[seed->pb2].rdname, ol);
}
} else if(wt->debug > 1){
fprintf(zmo_debug_out, "Keep %s, non-repetitive seed size %d\n", wt->reads->buffer[seed->pb2].rdname, ol);
}
*/
}
/*
if(wt->debug){
fprintf(zmo_debug_out, "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, pbid, 0);
//if(exists_u64hash(wt->closed_alns, val)) 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(wt->debug){
mseq = init_u8list(pb1->size); append_array_u8list(mseq, pb1->buffer, alen);
reset_simpMSA(msa, alen, pbid, mseq);