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wtdbg.h
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wtdbg.h
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/*
*
* Copyright (c) 2011, Jue Ruan <ruanjue@gmail.com>
*
*
* 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/>.
*/
#ifndef __WTDBG_H_RJ
#define __WTDBG_H_RJ
#include "kbm.h"
#include "kbmpoa.h"
#include "filewriter.h"
#include "pgzf.h"
#include <getopt.h>
#include <regex.h>
#define WT_MAX_RD 0x3FFFFFFF // 1 G
#define WT_MAX_RDLEN 0x00FFFFFF // 16 Mb
#define WT_MAX_RDBIN 0x0000FFFF // 64 K bins
#define WT_MAX_NODE 0x000000FFFFFFFFFFLLU
#define WT_MAX_EDGE 0x000000FFFFFFFFFFLLU
#define WT_MAX_NODE_EDGES 0xFFFF
#define WT_MAX_EDGE_COV 0x7FFF
typedef struct {
u8i rid:30, dir:1, beg:16, end:16, closed:1;
} rd_frg_t;
define_list(rdfrgv, rd_frg_t);
typedef struct {
u8i node;
u8i rid:30, dir:1, beg:16, end:16, closed:1;
} rd_reg_t;
define_list(rdregv, rd_reg_t);
typedef struct {
u8i rid:30, dir:1, beg:16, end:16, closed:1;
u8i read_link;
} rd_rep_t;
define_list(rdrepv, rd_rep_t);
typedef struct {
u8i node;
u8i rid:30, dir:1, beg:16, end:16, closed:1;
u8i read_link;
} reg_t;
define_list(regv, reg_t);
typedef struct { uint32_t x, y; } xy_t;
define_list(xyv, xy_t);
typedef struct { uint64_t idx:46, cnt:18; } vec_ref_t;
typedef struct { uint64_t idx:46, cnt:18; } ptr_ref_t;
typedef struct { uint64_t idx:46, cnt:18, fix:1, rank:45, score:18; } rnk_ref_t;
static const vec_ref_t VEC_REF_NULL = (vec_ref_t){0, 0};
static const ptr_ref_t PTR_REF_NULL = (ptr_ref_t){0, 0};
static const rnk_ref_t RNK_REF_NULL = (rnk_ref_t){0, 0, 0, 0, 0};
define_list(vecrefv, vec_ref_t);
define_list(ptrrefv, ptr_ref_t);
define_list(rnkrefv, rnk_ref_t);
#define ptrref_hashcode(E) u64hashcode((E).idx)
#define ptrref_hashequals(E1, E2) ((E1).idx == (E2).idx)
define_hashset(ptrrefhash, ptr_ref_t, ptrref_hashcode, ptrref_hashequals);
#define WT_EDGE_CLOSED_NULL 0
#define WT_EDGE_CLOSED_MASK 1
#define WT_EDGE_CLOSED_LESS 2
#define WT_EDGE_CLOSED_HARD 3
typedef struct {
uint64_t node1:45, dir1:1, dir2:1, status:1, closed:2, flag:2, cov:12;
uint64_t node2:45; int64_t off:19;
} edge_t;
define_list(edgev, edge_t);
static inline uint64_t _edge_hashcode(edge_t e){
const uint64_t m = 0xc6a4a7935bd1e995LLU;
const int r = 47;
uint64_t h = 1023 ^ (16 * m);
uint64_t k = (e.node1 << 1) | e.dir1;
k *= m;
k ^= k >> r;
k *= m;
h ^= k;
h *= m;
k = (e.node2 << 1) | e.dir2;
k *= m;
k ^= k >> r;
k *= m;
h ^= k;
h *= m;
h ^= h >> r;
h *= m;
h ^= h >> r;
return h;
}
#define EDGEHASH(idx) ((edgev *)set->userdata)->buffer[idx]
#define edge_hashcode(E) _edge_hashcode(EDGEHASH(E))
#define edge_hashequals(E1, E2) (EDGEHASH(E1).node1 == EDGEHASH(E2).node1 && EDGEHASH(E1).node2 == EDGEHASH(E2).node2 \
&& EDGEHASH(E1).dir1 == EDGEHASH(E2).dir1 && EDGEHASH(E1).dir2 == EDGEHASH(E2).dir2)
define_hashset(edgehash, uint64_t, edge_hashcode, edge_hashequals);
typedef struct { uint64_t idx:63, flg:1; uint64_t next; } edge_ref_t;
static const edge_ref_t EDGE_REF_NULL = (edge_ref_t){0x7FFFFFFFFFFFFFFLLU, 1, 0};
define_list(edgerefv, edge_ref_t);
#define MAX_REP_IDX MAX_U4
typedef struct {
u8i rep_idx:32;
u4i unvisit:16, cov:16;
u8i closed:1, single_in:1, bt_visit:45, rep_dir:1, bt_idx:16, init_end:1;
vec_ref_t regs;
ptr_ref_t edges[2];
} node_t;
define_list(nodev, node_t);
typedef struct {
u8i idx:39, flg:1, cnt:24;
} hit_lnk_t;
define_list(hitlnkv, hit_lnk_t);
typedef struct {
rd_frg_t frgs[2];
hit_lnk_t lnks[2]; // idx+flg: link, cnt[0]: mat, cnt[1]:cglen
} rd_hit_t;
define_list(rdhitv, rd_hit_t);
typedef struct {
u8i visit:63, flag:1;
hit_lnk_t hits; // point to the g->rdhits
int clps[2];
ptr_ref_t regs;
u2i corr_bincnt;
} read_t;
define_list(readv, read_t);
typedef struct {
u8i node;
//node_t *n;
edge_ref_t edges[2];
u4i dir:2, cov:30;
int off;
} trace_t;
define_list(tracev, trace_t);
#define WT_TRACE_MSG_ZERO 0
#define WT_TRACE_MSG_ONE 1
#define WT_TRACE_MSG_MORE 2
#define WT_TRACE_MSG_VISITED 3
#define WT_TRACE_MSG_UNDEF 4
typedef struct {
union {
struct {
u4i frg1:31, dir1:1;
u4i frg2:31, dir2:1;
};
u8i key;
};
u4i cov:13, flag:2, tidx1:8, tidx2:8, weak:1, closed:2;
b4i off;
} lnk_t;
define_list(lnkv, lnk_t);
#define lnk_hashcode(E) (E).key
#define lnk_hashequals(E1, E2) (E1).key == (E2).key
define_hashset(lnkhash, lnk_t, lnk_hashcode, lnk_hashequals);
typedef struct {
u8i toff:46, tcnt:18; // extended traces and core traces
u4i tx, ty; // core traces
ptr_ref_t lnks[2];
u4i len, length;
u8i rep_idx:48, unvisit:16;
u8i closed:1, single_in:1, bt_visit:46, rep_dir:1, bt_idx:16;
} frg_t;
define_list(frgv, frg_t);
typedef struct {
edge_ref_t lnks[2];
u4i frg;
u4i dir:2, cov:30;
int off;
u4i tx, ty;
} path_t;
define_list(pathv, path_t);
#define WT_PATH_MSG_ZERO 0
#define WT_PATH_MSG_ONE 1
#define WT_PATH_MSG_MORE 2
#define WT_PATH_MSG_VISITED 3
#define WT_PATH_MSG_UNDEF 4
typedef struct {
u8i node1:63, dir1:1;
u8i node2:63, dir2:1;
b8i off:42, len:22;
} seqlet_t;
define_list(seqletv, seqlet_t);
typedef struct {
KBM *kbm;
KBMPar *par;
regv *regs;
readv *reads;
rdhitv *rdhits;
BitsVec *cigars;
nodev *nodes;
edgev *edges;
edgehash *ehash;
edgerefv *erefs;
frgv *frgs;
lnkv *lnks;
edgerefv *lrefs;
tracev *traces;
u8i genome_size;
u4i corr_mode, corr_min, corr_max;
u4i corr_bsize, corr_bstep;
float corr_cov, corr_gcov;
int node_order, mem_stingy;
u4i n_fix, only_fix; // first n sequences are accurate contigs; only_fix means whether to include other pacbio sequenes
u4i reglen, regovl, bestn;
int min_node_mats;
int max_overhang, chainning_hits, uniq_hit;
float node_max_conflict; // 0.25
float node_merge_cutoff;
uint32_t max_node_cov, min_node_cov, exp_node_cov, min_edge_cov;
u4i max_node_cov_sg, max_sg_end;
int cut_tip;
int store_low_cov_edge;
int rep_filter, rep_detach;
uint32_t bub_step, tip_step, rep_step;
int min_ctg_len, min_ctg_nds, minimal_output;
vplist *utgs;
u4i major_nctg;
vplist *ctgs;
} Graph;
static const char *colors[2][2] = {{"blue", "green"}, {"red", "gray"}};
static inline Graph* init_graph(KBM *kbm){
Graph *g;
u4i rid;
g = malloc(sizeof(Graph));
g->kbm = kbm;
g->par = kbm->par;
g->regs = init_regv(32);
g->reads = init_readv(kbm->reads->size);
g->reads->size = kbm->reads->size;
for(rid=0;rid<g->reads->size;rid++){
g->reads->buffer[rid].clps[0] = 0;
g->reads->buffer[rid].clps[1] = g->kbm->reads->buffer[rid].rdlen / KBM_BIN_SIZE;
}
g->nodes = init_nodev(32);
g->rdhits = init_rdhitv(1024);
g->cigars = init_bitsvec(1024, 3);
g->edges = init_edgev(32);
g->ehash = init_edgehash(1023);
set_userdata_edgehash(g->ehash, g->edges);
g->erefs = init_edgerefv(32);
g->frgs = init_frgv(32);
g->lnks = init_lnkv(32);
g->lrefs = init_edgerefv(32);
g->traces = init_tracev(32);
g->genome_size = 1024 * 1024 * 1024LLU;
g->corr_mode = 0;
g->corr_min = 5;
g->corr_max = 10;
g->corr_cov = 0.75;
g->corr_gcov = 5.0;
g->corr_bsize = 2048;
g->corr_bstep = 2048 - 512;
g->node_order = 0;
g->n_fix = 0;
g->only_fix = 0;
g->reglen = 1024;
g->regovl = 256;
g->node_max_conflict = 0.25;
g->node_merge_cutoff = 0.8;
g->max_overhang = -1;
g->bestn = 0;
g->min_node_mats = 1;
g->chainning_hits = 0;
g->uniq_hit = 0;
g->min_node_cov = 4;
g->max_node_cov = 60;
g->exp_node_cov = 40; // expected node cov
g->min_edge_cov = 4;
g->max_node_cov_sg = 2;
g->max_sg_end = 5;
g->store_low_cov_edge = 1;
g->rep_filter = 1;
g->rep_detach = 1;
g->bub_step = 10;
g->tip_step = 5;
g->rep_step = 20;
g->cut_tip = 1;
g->min_ctg_len = 10000;
g->min_ctg_nds = 5;
g->minimal_output = 0;
g->utgs = init_vplist(32);
g->ctgs = init_vplist(32);
g->major_nctg = 0;
return g;
}
static inline void free_graph(Graph *g){
u8i i;
free_regv(g->regs);
free_readv(g->reads);
free_nodev(g->nodes);
free_rdhitv(g->rdhits);
free_bitsvec(g->cigars);
free_edgev(g->edges);
free_edgehash(g->ehash);
free_edgerefv(g->erefs);
free_frgv(g->frgs);
free_lnkv(g->lnks);
free_edgerefv(g->lrefs);
free_tracev(g->traces);
for(i=0;i<g->utgs->size;i++) free_tracev(g->utgs->buffer[i]);
free_vplist(g->utgs);
for(i=0;i<g->ctgs->size;i++) free_tracev(g->ctgs->buffer[i]);
free_vplist(g->ctgs);
free(g);
}
static inline int map2rdhits_graph(Graph *g, kbm_map_t *hit){
u4i k, f, d, p, n, add;
rd_hit_t *rh, *hp, *hn;
read_t *rd;
if(hit->mat == 0) return 0;
rh = next_ref_rdhitv(g->rdhits);
rh->frgs[0] = (rd_frg_t){hit->qidx, hit->qdir, hit->qb, hit->qe, 0};
rh->frgs[1] = (rd_frg_t){hit->tidx, hit->tdir, hit->tb, hit->te, 0};
rh->lnks[0].cnt = hit->mat;
rh->lnks[1].cnt = hit->cglen;
add = 0;
for(k=0;k<2;k++){
rd = ref_readv(g->reads, rh->frgs[k].rid);
hn = ref_rdhitv(g->rdhits, rd->hits.idx);
f = rd->hits.flg;
hp = NULL;
p = 0;
n = 1;
while(1){
if(hn->lnks[0].cnt <= rh->lnks[0].cnt){ // hit->mat
break;
}
p = f;
hp = hn;
if(hn->lnks[f].idx == 0) break;
f = hn->lnks[p].flg;
hn = ref_rdhitv(g->rdhits, hn->lnks[p].idx);
n ++;
}
if(g->bestn && n > g->bestn){
continue;
}
if(hp == NULL){
rh->lnks[k].idx = rd->hits.idx;
rh->lnks[k].flg = rd->hits.flg;
rd->hits.idx = offset_rdhitv(g->rdhits, rh);
rd->hits.flg = k;
} else {
rh->lnks[k].idx = hp->lnks[p].idx;
rh->lnks[k].flg = hp->lnks[p].flg;
hp->lnks[p].idx = offset_rdhitv(g->rdhits, rh);
hp->lnks[p].flg = k;
}
rd->hits.cnt ++;
if(g->bestn && rd->hits.cnt > g->bestn){
hn = rh;
p = k;
while(n < g->bestn){
f = hn->lnks[p].flg;
hn = ref_rdhitv(g->rdhits, hn->lnks[p].idx);
p = f;
n ++;
}
hp = hn;
f = p;
while(hn->lnks[f].idx){
d = hn->lnks[f].flg;
hn = ref_rdhitv(g->rdhits, hn->lnks[f].idx);
hn->frgs[f].closed = 1;
f = d;
}
hp->lnks[p].idx = 0;
hp->lnks[p].flg = 0;
rd->hits.cnt = n;
}
add ++;
}
if(add == 0){
trunc_rdhitv(g->rdhits, 1);
g->cigars->size -= hit->cglen;
}
return add;
}
static inline int is_dovetail_overlap(Graph *g, kbm_map_t *hit){
read_t *q, *t;
int overhangs[2][2];
q = ref_readv(g->reads, hit->qidx);
t = ref_readv(g->reads, hit->tidx);
overhangs[1][0] = hit->tb - t->clps[0];
overhangs[1][1] = (t->clps[1] - t->clps[0]) - hit->te;
if(hit->qdir){
overhangs[0][0] = (q->clps[1] - q->clps[0]) - hit->qe;
overhangs[0][1] = hit->qb;
} else {
overhangs[0][0] = hit->qb;
overhangs[0][1] = (q->clps[1] - q->clps[0]) - hit->qe;
}
if(overhangs[0][0] > g->max_overhang && overhangs[1][0] > g->max_overhang){
return 0;
}
if(overhangs[0][1] > g->max_overhang && overhangs[1][1] > g->max_overhang){
return 0;
}
return 1;
}
// qlen is measured by KBM_BIN_SIZE
static inline int hit2rdregs_graph(Graph *g, rdregv *regs, int qlen, kbm_map_t *hit, BitsVec *cigars, u4v *maps[3]){
KBM *kbm;
u8i ndoff;
u4i bpos[2][2], npos[2][2], clen, ndbeg, qn, j, qbincnt;
int tmp, bt, tlen, x, y, mat, beg, end, min_node_len, max_node_len;
int mask, closed;
kbm = g->kbm;
mask = 0;
if(g->max_overhang >= 0){
if(!is_dovetail_overlap(g, hit)){
mask = 1;
}
}
qn = g->reglen;
min_node_len = (qn - 1);
max_node_len = (qn + 1);
// translate into reverse sequence order
if(qlen == 0){
qbincnt = kbm->reads->buffer[hit->qidx].bincnt;
qlen = qbincnt;
} else if(qlen > kbm->reads->buffer[hit->qidx].bincnt){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
} else {
qbincnt = qlen;
}
tlen = kbm->reads->buffer[hit->tidx].bincnt;
if(hit->qdir){
tmp = qlen - hit->qb;
hit->qb = qlen - hit->qe;
hit->qe = tmp;
}
{
clear_u4v(maps[0]);
clear_u4v(maps[1]);
clear_u4v(maps[2]);
clen = hit->cglen;
x = -1; y = -1;
while(clen){
bt = get_bitsvec(cigars, hit->cgoff + clen - 1);
push_u4v(maps[2], !(bt >> 2));
bt = bt & 0x03;
switch(bt){
case 0: x ++; y ++; break;
case 1: x ++; break;
case 2: y ++; break;
}
push_u4v(maps[0], x);
push_u4v(maps[1], y);
clen --;
}
push_u4v(maps[0], x + 1);
push_u4v(maps[1], y + 1);
push_u4v(maps[2], 0);
#if DEBUG
if(x + 1 + hit->qb != hit->qe || y + 1 + hit->tb != hit->te){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
print_hit_kbm(g->kbm, g->kbm->reads->buffer[hit->qidx].tag, g->kbm->reads->buffer[hit->qidx].rdlen, hit, cigars, NULL, stderr);
abort();
}
#endif
}
bpos[0][0] = hit->qb;
bpos[0][1] = hit->qe;
bpos[1][0] = hit->tb;
bpos[1][1] = hit->te;
#if 0
fprintf(stdout, "BPOS\t%d\t%d\t%d\t%d\n", bpos[0][0], bpos[0][1], bpos[1][0], bpos[1][1]);
for(j=0;j<maps[0]->size;j++){
fprintf(stdout, "%d,%d\t", maps[0]->buffer[j], maps[1]->buffer[j]);
if((j % 10) == 9) fprintf(stdout, "\n");
}
fprintf(stdout, "\n");
#endif
{
ndoff = kbm->reads->buffer[hit->qidx].binoff;
if(hit->qdir){
ndbeg = qbincnt - bpos[0][0];
ndbeg = ndbeg % qn;
ndoff = ndoff + ((qbincnt - (ndbeg + bpos[0][0])) / qn) - 1;
} else {
ndbeg = (bpos[0][0] % qn)? qn - (bpos[0][0] % qn) : 0;
ndoff = ndoff + ((ndbeg + bpos[0][0]) / qn);
}
x = 0;
for(j=ndbeg+bpos[0][0];j+qn<=bpos[0][1];j+=qn){
mat = 0;
while(maps[0]->buffer[x] < j - bpos[0][0]){
x ++;
}
npos[0][0] = maps[1]->buffer[x];
while(maps[0]->buffer[x] == j - bpos[0][0]){
if(maps[2]->buffer[x]) mat ++;
x ++;
}
npos[0][1] = maps[1]->buffer[x];
while(maps[0]->buffer[x] < j + qn - 1 - bpos[0][0]){
if(maps[2]->buffer[x]) mat ++;
x ++;
}
npos[1][0] = maps[1]->buffer[x];
while(maps[0]->buffer[x + 1] == j + qn - 1 - bpos[0][0]){
if(maps[2]->buffer[x]) mat ++;
x ++;
}
npos[1][1] = maps[1]->buffer[x];
// TODO: arbitrarily use outer boundary as matched region, need to test its effect
// TODO: whether to remove regs outside clps
if(mat >= g->min_node_mats){
beg = (npos[0][0] + bpos[1][0]);
end = (npos[1][1] + bpos[1][0] + 1);
if(end - beg >= min_node_len && end - beg <= max_node_len){
closed = 0;
} else {
closed = 1;
}
#if DEBUG
if(beg >= end){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
}
#endif
push_rdregv(regs, (rd_reg_t){ndoff, hit->tidx, hit->qdir, beg, end, mask | closed});
}
if(hit->qdir){
ndoff --;
} else {
ndoff ++;
}
#if 0
rd_reg_t *rg = ref_rdregv(regs, regs->size - 1);
fprintf(stdout, "NPOS\tX=%d,%d\tY=%d,%d\t%d\t%d\t%d\t%d\n", j, j - bpos[0][0], j + qn - 1, j + qn - 1 - bpos[0][0], npos[0][0], npos[0][1], npos[1][0], npos[1][1]);
fprintf(stdout, "REG\t%llu\t%s\t%c\t%d\t%d\t%d\n", rg->node, kbm->reads->buffer[rg->rid].tag, "+-"[rg->dir], rg->beg, rg->end, rg->end - rg->beg);
#endif
}
}
if(!g->corr_mode){
ndoff = kbm->reads->buffer[hit->tidx].binoff;
ndbeg = (bpos[1][0] % qn)? qn - (bpos[1][0] % qn): 0;
ndoff = ndoff + ((ndbeg + bpos[1][0]) / qn);
x = 0;
for(j=ndbeg+bpos[1][0];j+qn<=bpos[1][1];j+=qn){
mat = 0;
while(maps[1]->buffer[x] < j - bpos[1][0]){
x ++;
}
npos[0][0] = maps[0]->buffer[x];
while(maps[1]->buffer[x] == j - bpos[1][0]){
if(maps[2]->buffer[x]) mat ++;
x ++;
}
npos[0][1] = maps[0]->buffer[x];
while(maps[1]->buffer[x] < j + qn - 1 - bpos[1][0]){
if(maps[2]->buffer[x]) mat ++;
x ++;
}
npos[1][0] = maps[0]->buffer[x];
while(maps[1]->buffer[x + 1] == j + qn - 1 - bpos[1][0]){
if(maps[2]->buffer[x]) mat ++;
x ++;
}
npos[1][1] = maps[0]->buffer[x];
// TODO: arbitrarily use outer boundary as matched region, need to test its effect
if(mat >= g->min_node_mats){
if(hit->qdir){
beg = qlen - (npos[1][1] + bpos[0][0] + 1);
end = qlen - (npos[0][0] + bpos[0][0]);
} else {
beg = (npos[0][0] + bpos[0][0]);
end = (npos[1][1] + bpos[0][0] + 1);
}
if(end - beg >= min_node_len && end - beg <= max_node_len){
closed = 0;
} else {
closed = 1;
}
#if DEBUG
if(beg >= end){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
}
#endif
push_rdregv(regs, (rd_reg_t){ndoff, hit->qidx, hit->qdir, beg, end, mask | closed});
#if 0
fprintf(stdout, "NPOS\tX=%d,%d\tY=%d,%d\t%d\t%d\t%d\t%d\n", j, j - bpos[1][0], j + qn - 1, j + qn - 1 - bpos[1][0], npos[0][0], npos[0][1], npos[1][0], npos[1][1]);
rd_reg_t *rg = ref_rdregv(regs, regs->size - 1);
fprintf(stdout, "REG\t%llu\t%s\t%c\t%d\t%d\t%d\n", rg->node, kbm->reads->buffer[rg->rid].tag, "+-"[rg->dir], rg->beg, rg->end, rg->end - rg->beg);
#endif
}
ndoff ++;
}
}
if(hit->qdir){
tmp = qlen - hit->qb;
hit->qb = qlen - hit->qe;
hit->qe = tmp;
}
return !mask;
}
thread_beg_def(mdbg);
Graph *g;
KBMAux *aux;
CTGCNS *cc;
reg_t reg;
rdregv *regs;
BitVec *rdflags;
u4i beg, end;
int raw;
FILE *alno;
int task;
thread_end_def(mdbg);
thread_beg_func(mdbg);
Graph *g;
KBM *kbm;
KBMAux *aux;
rdregv *regs;
BitVec *rdflags;
u4v *maps[3];
volatile reg_t *reg;
g = mdbg->g;
kbm = g->kbm;
reg = (reg_t*)&mdbg->reg;
aux = mdbg->aux;
regs = mdbg->regs;
rdflags = mdbg->rdflags;
maps[0] = init_u4v(32);
maps[1] = init_u4v(32);
maps[2] = init_u4v(32);
thread_beg_loop(mdbg);
if(mdbg->task == 1){
if(reg->closed) continue;
if(g->corr_mode){
if(map_kbmpoa(mdbg->cc, aux, kbm->reads->buffer[reg->rid].tag, reg->rid, kbm->rdseqs, kbm->reads->buffer[reg->rid].rdoff + reg->beg, reg->end - reg->beg, g->corr_min, g->corr_max, g->corr_cov, NULL) == 0){
clear_kbmmapv(aux->hits);
}
} else {
query_index_kbm(aux, NULL, reg->rid, kbm->rdseqs, kbm->reads->buffer[reg->rid].rdoff + reg->beg, reg->end - reg->beg);
map_kbm(aux);
}
sort_array(aux->hits->buffer, aux->hits->size, kbm_map_t, num_cmpgt(b.mat, a.mat));
}
thread_end_loop(mdbg);
free_u4v(maps[0]);
free_u4v(maps[1]);
free_u4v(maps[2]);
thread_end_func(mdbg);
typedef struct {
int pos:19;
u4i dir:1, spur:1, dep:11;
} rd_clp_t;
define_list(rdclpv, rd_clp_t);
static inline void clip_read_algo(int clps[2], rdclpv *brks, rdclpv *chis, int avg_dep, int min_dep){
rd_clp_t *c;
u4i i;
int dep, x, y, max, mx, my;
sort_array(brks->buffer, brks->size, rd_clp_t, num_cmpgt((a.pos << 1) | a.dir, (b.pos << 1) | b.dir));
x = y = 0; max = 0; dep = 0; mx = my = 0;
for(i=0;i<brks->size;i++){
c = ref_rdclpv(brks, i);
if(dep >= min_dep){
y = c->pos;
if(y - x > max){
max = y - x;
mx = x;
my = y;
}
}
if(c->dir){ // end of overlap
c->dep = dep;
dep --;
} else {
dep ++;
c->dep = dep;
if(dep == min_dep){
x = c->pos;
}
}
if(c->spur){
push_rdclpv(chis, (rd_clp_t){c->pos - KBM_BIN_SIZE, 0, 0, c->dep});
push_rdclpv(chis, (rd_clp_t){c->pos - 1, 1, 0, c->dep});
push_rdclpv(chis, (rd_clp_t){c->pos, 0, 1, c->dep});
push_rdclpv(chis, (rd_clp_t){c->pos + KBM_BIN_SIZE, 1, 0, c->dep});
}
}
clps[0] = mx / KBM_BIN_SIZE;
clps[1] = my / KBM_BIN_SIZE;
if((int)chis->size < avg_dep){
return;
}
sort_array(chis->buffer, chis->size, rd_clp_t, num_cmpgtx(a.pos, b.pos, b.dir, a.dir));
dep = 0; max = 0; mx = 0;
for(i=0;i<chis->size;i++){
c = ref_rdclpv(chis, i);
if(c->dir){
if(c->spur){
if(dep >= max){
max = dep;
mx = i;
}
}
dep --;
} else {
dep ++;
if(c->spur){
if(dep >= max){
max = dep;
mx = i;
}
}
}
}
if(max * 2 < avg_dep){
return;
}
c = ref_rdclpv(chis, mx);
if(c->dep >= avg_dep){
return;
}
if(2 * c->dep > max + 1){
return;
}
if(c->pos <= clps[0] * KBM_BIN_SIZE || c->pos >= clps[1] * KBM_BIN_SIZE){
return;
}
if(c->pos - clps[0] > clps[1] - c->pos){
clps[1] = (c->pos + 1) / KBM_BIN_SIZE;
} else {
clps[0] = (c->pos + 1) / KBM_BIN_SIZE;
}
}
static inline void clip_read_core(Graph *g, u4i rid, hitlnkv *lnks, rdclpv *brks, rdclpv *chis){
read_t *rd;
hit_lnk_t *lnk;
rd_hit_t *hit;
rd_frg_t *f1, *f2;
u4i i;
int rlen, dlen, margin, min_dep, dep, avg, x, y;
rd = ref_readv(g->reads, rid);
rlen = g->kbm->reads->buffer[rid].bincnt;
if(rlen == 0){
return;
}
lnk = &rd->hits;
clear_rdclpv(brks);
margin = g->max_overhang > 0? g->max_overhang : 4;
min_dep = 2;
dep = 0;
clear_hitlnkv(lnks);
while(lnk->idx){
hit = ref_rdhitv(g->rdhits, lnk->idx);
f1 = hit->frgs + lnk->flg;
if(f1->closed == 0) push_hitlnkv(lnks, *lnk);
lnk = hit->lnks + lnk->flg;
}
for(i=0;i<lnks->size;i++){
lnk = ref_hitlnkv(lnks, i);
hit = ref_rdhitv(g->rdhits, lnk->idx);
f1 = hit->frgs + lnk->flg;
if(f1->closed == 0){
// whether be contained
if(f1->beg <= margin && f1->end + margin >= rlen){
rd->clps[0] = 0;
rd->clps[1] = rlen;
return;
}
f2 = hit->frgs + !lnk->flg;
dlen = g->kbm->reads->buffer[f2->rid].bincnt * KBM_BIN_SIZE;
if(f1->dir ^ f2->dir){
x = (f1->beg > margin && f2->end + margin < dlen);
y = (f1->end + margin < rlen && f2->beg > margin);
} else {
x = (f1->beg > margin && f2->beg > margin);
y = (f1->end + margin < rlen && f2->end + margin < dlen);
}
if(x && y){
//push_rdclpv(brks, (rd_clp_t){f1->beg, 0, 1, 0});
//push_rdclpv(brks, (rd_clp_t){f1->end, 1, 1, 0});
} else if(x){
push_rdclpv(brks, (rd_clp_t){f1->beg * KBM_BIN_SIZE, 0, 1, 0});
push_rdclpv(brks, (rd_clp_t){f1->end * KBM_BIN_SIZE, 1, 0, 0});
} else if(y){
push_rdclpv(brks, (rd_clp_t){f1->beg * KBM_BIN_SIZE, 0, 0, 0});
push_rdclpv(brks, (rd_clp_t){f1->end * KBM_BIN_SIZE, 1, 1, 0});
} else {
dep += f1->end - f1->beg;
push_rdclpv(brks, (rd_clp_t){f1->beg * KBM_BIN_SIZE, 0, 0, 0});
push_rdclpv(brks, (rd_clp_t){f1->end * KBM_BIN_SIZE, 1, 0, 0});
}
}
}
clear_rdclpv(chis);
avg = (dep + rlen - 1) / rlen;
clip_read_algo(rd->clps, brks, chis, avg, min_dep);
}
thread_beg_def(mclp);
Graph *g;
thread_end_def(mclp);
thread_beg_func(mclp);
rdclpv *brks, *chis;
hitlnkv *lnks;
u4i rid;
brks = init_rdclpv(32);
chis = init_rdclpv(32);
lnks = init_hitlnkv(32);
thread_beg_loop(mclp);
for(rid=mclp->t_idx;rid<mclp->g->reads->size;rid+=mclp->n_cpu){
clip_read_core(mclp->g, rid, lnks, brks, chis);
}
thread_end_loop(mclp);
free_rdclpv(brks);
free_rdclpv(chis);
free_hitlnkv(lnks);
thread_end_func(mclp);
static inline u8i check_read_reg_conflict_core(Graph *g, rd_reg_t *hit, int *conflict){
read_t *rd;
reg_t *reg;
u8i idx, pre;
int x, y;
rd = ref_readv(g->reads, hit->rid);
idx = rd->regs.idx;
pre = 0;
*conflict = 0;
while(idx){
reg = ref_regv(g->regs, idx);
if(hit->beg >= reg->beg) pre = idx;
idx = reg->read_link;
if(hit->end <= reg->beg) break;
if(hit->beg >= reg->end) continue;
if(reg->closed) continue;
if(hit->beg <= reg->beg){
x = reg->beg;
if(hit->end >= reg->end){
y = reg->end;
} else y = hit->end;
} else {
x = hit->beg;
if(hit->end <= reg->end){
y = hit->end;
} else y = reg->end;
}
if(x < y){
if(x + (int)g->regovl < y) *conflict = 1;
}
}
return pre;
}
thread_beg_def(mupd);
Graph *g;
rdregv *regs;
rnk_ref_t *nd;
u8v *ins;
u8i vt;
thread_end_def(mupd);
thread_beg_func(mupd);
Graph *g;
rdregv *regs;
rd_reg_t *hit;
u8i pre;
u4i i;
int conflict;
g = mupd->g;
regs = mupd->regs;
thread_beg_loop(mupd);
if(mupd->nd == NULL) continue;
clear_u8v(mupd->ins);
if(1){
for(i=1;i<mupd->nd->cnt;i++){
if(regs->buffer[mupd->nd->idx + i].rid == regs->buffer[mupd->nd->idx + i - 1].rid){
regs->buffer[mupd->nd->idx + i].closed = 1;
regs->buffer[mupd->nd->idx + i - 1].closed = 1;
}
}
}
for(i=0;i<mupd->nd->cnt;i++){
hit = ref_rdregv(regs, mupd->nd->idx + i);
conflict = 0;
pre = check_read_reg_conflict_core(g, hit, &conflict);
if(conflict){
hit->closed = 1;
}
push_u8v(mupd->ins, pre);
}
thread_end_loop(mupd);
thread_end_func(mupd);
//TODO: reg_t to store regs, sort them by rank, and sort them by rid in another u4i/u8i array
//TODO: fast generate nodes and read_link, then select important intervals
static inline void mul_update_regs_graph(Graph *g, rdregv *regs, rnkrefv *nds, u4i ncpu, u8i upds[3]){
u8i idx, vt;
u4i i, j, pass;
read_t *rd;
node_t *n;
reg_t *reg, *r;
rd_reg_t *hit;
int conflict, closed;
thread_prepare(mupd);
for(i=0;i<g->reads->size;i++){
g->reads->buffer[i].visit = 0; // in which round did the read be touched
}
encap_regv(g->regs, regs->size + 1); // make sure next_ref_regv in this function is thread-safe
thread_beg_init(mupd, ncpu);
mupd->g = g;
mupd->regs = regs;
mupd->nd = NULL;
mupd->ins = init_u8v(64);
mupd->vt = 0;
thread_end_init(mupd);
vt = 1;
upds[0] = upds[1] = upds[2] = 0;
for(idx=0;idx<nds->size+ncpu;idx++){
thread_wait_next(mupd);
if(mupd->nd){
pass = 0;
for(j=0;j<mupd->nd->cnt;j++){
hit = ref_rdregv(regs, mupd->nd->idx + j);
rd = ref_readv(g->reads, hit->rid);
if(rd->visit >= mupd->vt){ // previous node had changed the layout of this read, need to check conflict again
mupd->ins->buffer[j] = check_read_reg_conflict_core(g, hit, &conflict);
if(conflict){
hit->closed = 1;
}
}
rd->visit = idx;
if(hit->closed == 0) pass ++;
}
do {
closed = 0;
if(0 && mupd->nd->cnt > g->max_node_cov){
// Repetitive nodes should be in graph to avoid mis-assembling
upds[1] ++;
closed = 1;
continue;
}
if(mupd->nd->fix){
if(pass == 0){
upds[1] ++;
closed = 1;
continue;
} else {
upds[0] ++;
}
} else {
if(pass < g->min_node_cov || pass < (u4i)(mupd->nd->cnt * (1 - g->node_max_conflict))){
upds[1] ++;
closed = 1;
continue;
} else {
upds[0] ++;
}
}