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poacns.h
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poacns.h
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/*
*
* Copyright (c) 2018, 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/>.
*/
#ifndef PO_MSA_CNS_RJ_H
#define PO_MSA_CNS_RJ_H
#include "bit2vec.h"
#include "dna.h"
#include "chararray.h"
#include "list.h"
#include "hashset.h"
#include <emmintrin.h>
#include <tmmintrin.h>
#if __BYTE_ORDER == 1234
//#pragma message(" ** " __FILE__ " has been tested in LITTLE_ENDIAN **\n")
#else
#pragma message(" ** " __FILE__ " hasn't been tested in BIG_ENDIAN **\n")
#endif
static int cns_debug = 0;
#define POG_RDLEN_MAX 0x7FF8
#define POG_RDCNT_MAX 0x3FFF
#define POG_BASEWIDTH 3
#define POG_BASEMAX 0x3F
#define POG_HEAD_NODE 0
#define POG_TAIL_NODE 1
#define POG_DP_BT_M 0
#define POG_DP_BT_I 1
#define POG_DP_BT_D 2
#define POG_ALNMODE_OVERLAP 0
#define POG_ALNMODE_GLOBAL 1
#define POG_VST_MAX MAX_U2
#define POG_SCORE_MIN (-(MAX_B2 >> 1))
typedef struct {
u2i rid, pos, base;
u2i rbeg, rend, rmax;
u2i nin, vst;
u4i edge, erev;
u4i aligned;
union {
u4i aux;
u4i bpos; // backbone pos
};
u4i coff;
union {
u8i flag;
struct { u4i roff, voff; };
};
} pog_node_t;
define_list(pognodev, pog_node_t);
typedef struct {
u4i node;
u4i cov:31, is_aux:1;
u4i next;
} pog_edge_t;
define_list(pogedgev, pog_edge_t);
typedef struct {
int cnsmode; // 0: gen_cns_pog, 1: dp_call_cns_pog
int refmode;
int alnmode;
int tribase;
int sse;
int near_dialog;
int W_score;
int W, rW, cW; // 160, 16, 8
int M, X, I, D, E;
float H; // homopolymer merge
int T; // bonus for end
u4i msa_min_cnt;
float msa_min_freq;
} POGPar;
static const POGPar DEFAULT_POG_PAR = (POGPar){0, 0, POG_ALNMODE_OVERLAP, 0, 1, 0, 0, 160, 16, 8, 2, -5, -2, -4, -1, -3, 20, 3, 0.5};
typedef struct {
u4i coff:29, bt:3;
float max;
} pog_cns_t;
typedef struct {
SeqBank *seqs;
u2v *sbegs, *sends; // suggested [beg, end) on ref(1st seq) in reference-based mode
pognodev *nodes;
pogedgev *edges;
POGPar *par;
b2v *qprof;
b2v *rows;
u4v *rowr;
b2v *btds;
u2v *btvs;
u4v *btxs;
u4v *stack;
u2i backbone;
u4i msa_len;
u1v *msa;
u2v *bcnts[7];
u2v *hcovs;
u1v *cbts;
BaseBank *cns;
u8i ncall;
} POG;
static inline POG* init_pog(POGPar par){
POG *g;
g = malloc(sizeof(POG));
g->seqs = init_seqbank();
g->sbegs = init_u2v(32);
g->sends = init_u2v(32);
g->nodes = init_pognodev(16 * 1024);
g->edges = init_pogedgev(16 * 1024);
g->par = malloc(sizeof(POGPar));
memcpy(g->par, &par, sizeof(POGPar));
g->qprof = init_b2v(4 * 1024);
g->rows = init_b2v(16 * 1024);
g->rowr = init_u4v(64);
g->btds = init_b2v(16 * 1024);
g->btvs = init_u2v(8 * 1024 * 1024);
g->btxs = init_u4v(1024);
g->stack = init_u4v(32);
g->backbone = 0;
g->msa_len = 0;
g->msa = init_u1v(16 * 1024);
g->bcnts[0] = init_u2v(4 * 1024);
g->bcnts[1] = init_u2v(4 * 1024);
g->bcnts[2] = init_u2v(4 * 1024);
g->bcnts[3] = init_u2v(4 * 1024);
g->bcnts[4] = init_u2v(4 * 1024);
g->bcnts[5] = init_u2v(4 * 1024);
g->bcnts[6] = init_u2v(4 * 1024);
g->hcovs = init_u2v(4 * 1024);
g->cbts = init_u1v(5 * 2 * 1024);
g->cns = init_basebank();
g->ncall = 0;
return g;
}
static inline void renew_pog(POG *g){
free_seqbank(g->seqs); g->seqs = init_seqbank();
renew_u2v(g->sbegs, 32);
renew_u2v(g->sends, 32);
renew_pognodev(g->nodes, 16 * 1024);
renew_pogedgev(g->edges, 16 * 1024);
renew_b2v(g->qprof, 4 * 1024);
renew_b2v(g->rows, 16 * 1024);
renew_u4v(g->rowr, 64);
renew_b2v(g->btds, 16 * 1024);
renew_u2v(g->btvs, 8 * 1024 * 1024);
renew_u4v(g->btxs, 16 * 1024);
renew_u4v(g->stack, 32);
renew_u1v(g->msa, 16 * 1024);
renew_u2v(g->bcnts[0], 4 * 1024);
renew_u2v(g->bcnts[1], 4 * 1024);
renew_u2v(g->bcnts[2], 4 * 1024);
renew_u2v(g->bcnts[3], 4 * 1024);
renew_u2v(g->bcnts[4], 4 * 1024);
renew_u2v(g->bcnts[5], 4 * 1024);
renew_u2v(g->bcnts[6], 4 * 1024);
renew_u2v(g->hcovs, 4 * 1024);
renew_u1v(g->cbts, 5 * 2 * 1024);
free_basebank(g->cns); g->cns = init_basebank();
}
static inline void free_pog(POG *g){
free_seqbank(g->seqs);
free_u2v(g->sbegs);
free_u2v(g->sends);
free_pognodev(g->nodes);
free_pogedgev(g->edges);
free_b2v(g->qprof);
free_b2v(g->rows);
free_u4v(g->rowr);
free_b2v(g->btds);
free_u2v(g->btvs);
free_u4v(g->btxs);
free_u4v(g->stack);
free_u1v(g->msa);
free_u2v(g->bcnts[0]);
free_u2v(g->bcnts[1]);
free_u2v(g->bcnts[2]);
free_u2v(g->bcnts[3]);
free_u2v(g->bcnts[4]);
free_u2v(g->bcnts[5]);
free_u2v(g->bcnts[6]);
free_u2v(g->hcovs);
free_u1v(g->cbts);
free_basebank(g->cns);
free(g->par);
free(g);
}
static inline void push_pog_core(POG *g, char *seq, u4i len, u2i refbeg, u2i refend){
if(g->seqs->nseq < POG_RDCNT_MAX){
len = num_min(len, POG_RDLEN_MAX);
push_seqbank(g->seqs, NULL, 0, seq, len);
push_u2v(g->sbegs, refbeg);
push_u2v(g->sends, refend);
}
}
static inline void push_pog(POG *g, char *seq, u1i len){ push_pog_core(g, seq, len, 0, 0); }
static inline void fwdbitpush_pog_core(POG *g, u8i *bits, u8i off, u4i len, u2i refbeg, u2i refend){
if(g->seqs->nseq < POG_RDCNT_MAX){
len = num_min(len, POG_RDLEN_MAX);
fwdbitpush_seqbank(g->seqs, NULL, 0, bits, off, len);
push_u2v(g->sbegs, refbeg);
push_u2v(g->sends, refend);
}
}
static inline void fwdbitpush_pog(POG *g, u8i *bits, u8i off, u4i len){ fwdbitpush_pog_core(g, bits, off, len, 0, 0); }
static inline void revbitpush_pog_core(POG *g, u8i *bits, u8i off, u4i len, u2i refbeg, u2i refend){
if(g->seqs->nseq < POG_RDCNT_MAX){
len = num_min(len, POG_RDLEN_MAX);
revbitpush_seqbank(g->seqs, NULL, 0, bits, off, len);
push_u2v(g->sbegs, refbeg);
push_u2v(g->sends, refend);
}
}
static inline void revbitpush_pog(POG *g, u8i *bits, u8i off, u4i len){ revbitpush_pog_core(g, bits, off, len, 0, 0); }
static inline void print_dot_pog(POG *g, FILE *out){
pog_node_t *n;
pog_edge_t *e;
u4i nidx, eidx;
fprintf(out, "digraph {\n");
fprintf(out, "rankdir=LR\n");
fprintf(out, "N0 [label=\"BEG\"]\n");
fprintf(out, "N1 [label=\"END\"]\n");
for(nidx=POG_TAIL_NODE+1;nidx<g->nodes->size;nidx++){
n = ref_pognodev(g->nodes, nidx);
fprintf(out, "N%u [label=R%u_%u_%c]\n", nidx, n->rid, n->pos, bit_base_table[(n->base) & 0x03]);
}
for(nidx=0;nidx<g->nodes->size;nidx++){
n = ref_pognodev(g->nodes, nidx);
if(n->aligned != nidx){
fprintf(out, "N%u -> N%u [color=magenta style=dashed]\n", nidx, n->aligned);
}
eidx = n->edge;
while(eidx){
e = ref_pogedgev(g->edges, eidx);
#if DEBUG
if(e->next == eidx){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
}
#endif
eidx = e->next;
if(e->is_aux) continue;
fprintf(out, "N%u -> N%u [label=%u]\n", nidx, e->node, e->cov);
}
}
fprintf(out, "}\n");
}
static inline void fprint_dot_pog(POG *g, char *prefix, char *suffix){
FILE *out;
out = open_file_for_write(prefix, suffix, 1);
print_dot_pog(g, out);
fclose(out);
}
static inline void print_vstdot_pog(POG *g, char *fname){
FILE *out;
pog_node_t *n;
pog_edge_t *e;
u4i nidx, eidx;
out = open_file_for_write(fname, NULL, 1);
fprintf(out, "digraph {\n");
for(nidx=0;nidx<g->nodes->size;nidx++){
n = ref_pognodev(g->nodes, nidx);
if(nidx && n->vst == 0) continue;
fprintf(out, "N%u [label=\"N%u:%u:%u:%d\"]\n", nidx, nidx, n->aux, n->nin, n->vst);
eidx = n->edge;
while(eidx){
e = ref_pogedgev(g->edges, eidx);
eidx = e->next;
if(e->is_aux) continue;
fprintf(out, "N%u -> N%u [label=%u]\n", nidx, e->node, e->cov);
}
}
fprintf(out, "}\n");
fclose(out);
}
static inline void print_seqs_pog(POG *g, char *prefix, char *suffix){
FILE *out;
u4i i;
out = open_file_for_write(prefix, suffix, 1);
for(i=0;i<g->seqs->nseq;i++){
fprintf(out, ">S%u len=%u\n", i, g->seqs->rdlens->buffer[i]);
println_fwdseq_basebank(g->seqs->rdseqs, g->seqs->rdoffs->buffer[i], g->seqs->rdlens->buffer[i], out);
}
fclose(out);
}
static inline void print_msa_pog(POG *g, FILE *out){
char *str;
u1i *cns;
u4i i, j, b, e, c, n;
str = malloc(g->msa_len + 1);
fprintf(out, "[POS] ");
for(i=j=0;i<g->msa_len;i++){
if((i % 10) == 0){
fprintf(out, "|%04u", i + 1);
j += 5;
} else if(i >= j){
putc(' ', out);
j ++;
}
}
fputc('\n', out);
for(i=0;i<g->seqs->nseq+1;i++){
if(i == g->seqs->nseq){
fprintf(out, "[CNS] ");
} else {
fprintf(out, "[%03u] ", i);
}
b = i * g->msa_len;
e = b + g->msa_len;
n = 0;
for(j=b;j<e;j++){
c = g->msa->buffer[j];
if(c < 4) n ++;
str[j-b] = "ACGT-acgt*"[c];
//fputc("ACGT-"[c], out);
}
str[e-b] = 0;
fputs(str, out);
if(i == g->seqs->nseq){
fprintf(out, "\t%u\t%u\n", (u4i)g->cns->size, n);
} else {
fprintf(out, "\t%u\t%u\n", g->seqs->rdlens->buffer[i], n);
}
}
fprintf(out, "[POS] ");
cns = ref_u1v(g->msa, g->msa_len * g->seqs->nseq);
for(i=j=b=0;i<g->msa_len;i++){
if(cns[i] < 4){
j ++;
if((j % 10) == 1){
while(b < i){
fputc(' ', out);
b ++;
}
fprintf(out, "|%04u", j);
b += 5;
}
}
}
fprintf(out, "\n");
if(1){
u4i divs[5];
u2i *hcovs;
hcovs = g->hcovs->buffer;
divs[0] = 10000;
divs[1] = 1000;
divs[2] = 100;
divs[3] = 10;
divs[4] = 1;
for(i=0;i<4;i++){
for(j=0;j<g->msa_len;j++){
if(hcovs[j] < divs[i + 1]){
str[j] = ' ';
} else {
str[j] = '0' + ((hcovs[j] % divs[i]) / divs[i + 1]);
}
}
str[j] = 0;
fprintf(out, "[%c ] %s\n", "HCOV"[i], str);
}
}
free(str);
}
static inline pog_node_t* add_node_pog(POG *g, u2i rid, u2i pos, u2i base){
pog_node_t *u;
u = next_ref_pognodev(g->nodes);
ZEROS(u);
u->rid = rid;
u->pos = pos;
u->base = base;
u->aligned = offset_pognodev(g->nodes, u);
return u;
}
static inline pog_edge_t* add_edge_pog(POG *g, pog_node_t *u, pog_node_t *v, int cov, int is_aux){
pog_edge_t *e, *f, *p;
u4i eidx;
#if DEBUG
if(u == v){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
}
#endif
if(u->edge == 0){
e = next_ref_pogedgev(g->edges);
u->edge = offset_pogedgev(g->edges, e);
e->node = offset_pognodev(g->nodes, v);
e->cov = cov;
e->is_aux = is_aux;
e->next = 0;
v->nin ++;
return e;
} else {
e = f = p = NULL;
encap_pogedgev(g->edges, 1);
eidx = u->edge;
while(eidx){
f = ref_pogedgev(g->edges, eidx);
eidx = f->next;
if(f->node == offset_pognodev(g->nodes, v)){
e = f;
break;
}
p = f;
}
if(e == NULL){
e = next_ref_pogedgev(g->edges);
e->node = offset_pognodev(g->nodes, v);
e->cov = cov;
e->is_aux = is_aux;
e->next = 0;
v->nin ++;
} else {
e->is_aux &= is_aux;
e->cov += cov;
if(cov == 0){
return e;
} else if(p == NULL){
return e;
}
// detach e from u->edge
p->next = e->next;
e->next = 0;
}
f = ref_pogedgev(g->edges, u->edge);
if(e->cov > f->cov){
e->next = u->edge;
u->edge = offset_pogedgev(g->edges, e);
} else {
while(f->next){
if(ref_pogedgev(g->edges, f->next)->cov < e->cov){
break;
}
f = ref_pogedgev(g->edges, f->next);
}
e->next = f->next;
f->next = offset_pogedgev(g->edges, e);
}
return e;
}
}
static inline pog_node_t* merge_node_pog(POG *g, pog_node_t *x, pog_node_t *u){
pog_node_t *v, *w;
pog_edge_t *e;
u4i xidx, eidx;
xidx = offset_pognodev(g->nodes, x);
do {
v = ref_pognodev(g->nodes, xidx);
if(v->nin && v->base == u->base){
eidx = u->edge;
while(eidx){
e = ref_pogedgev(g->edges, eidx);
eidx = e->next;
w = ref_pognodev(g->nodes, e->node);
add_edge_pog(g, v, w, e->cov, e->is_aux);
w->nin --; // will delete e
}
u->edge = 0;
break;
}
v = NULL;
} while(xidx != offset_pognodev(g->nodes, x));
u->aligned = x->aligned;
x->aligned = offset_pognodev(g->nodes, u);
return v? v : u;
}
static inline void beg_pog_core(POG *g, BaseBank *cns, u8i off, u2i len, int clear_all){
pog_node_t *head, *tail, *u, *v;
pog_edge_t *e;
u4i i, bb, bk;
g->ncall ++;
if((g->ncall % 16) == 0){
renew_pog(g);
}
clear_and_encap_pognodev(g->nodes, 2 + len);
clear_pogedgev(g->edges);
ZEROS(next_ref_pogedgev(g->edges));
head = next_ref_pognodev(g->nodes);
ZEROS(head);
if(g->par->tribase){
head->base = POG_BASEMAX + 1;
} else {
head->base = 4;
}
head->aligned = POG_HEAD_NODE;
tail = next_ref_pognodev(g->nodes);
ZEROS(tail);
if(g->par->tribase){
tail->base = POG_BASEMAX + 1;
} else {
tail->base = 4;
}
tail->aligned = POG_TAIL_NODE;
u = head;
bk = 0;
// add backbone nodes
g->backbone = len;
for(i=0;i<len;i++){
bb = get_basebank(cns, off + i);
if(g->par->tribase){
bk = ((bk << 2) | bb) & POG_BASEMAX;
} else {
bk = bb;
}
v = add_node_pog(g, g->seqs->nseq, i, bk);
v->bpos = i;
e = add_edge_pog(g, u, v, 0, 1);
u = v;
}
e = add_edge_pog(g, u, tail, 0, 1);
if(clear_all){
clear_seqbank(g->seqs);
clear_u2v(g->sbegs);
clear_u2v(g->sends);
clear_basebank(g->cns);
}
}
static inline void beg_pog(POG *g){
beg_pog_core(g, NULL, 0, 0, 1);
}
static inline void prepare_rd_align_pog(POG *g, u2i rid){
pog_node_t *u, *v;
pog_edge_t *e;
b2i *row, *btds;
u8i rmax;
u4i seqoff, seqlen, seqlex, slen, seqinc;
u4i nidx, eidx, i, j, bb;
seqoff = g->seqs->rdoffs->buffer[rid];
seqlen = g->seqs->rdlens->buffer[rid];
seqlex = roundup_times(seqlen, 8); // 128 = 8 * sizeof(b2i)
slen = seqlex >> 3;
seqinc = seqlex + 8; // seqlex, max_idx, beg, end, and paddings
// init graph
encap_pognodev(g->nodes, seqlen + 2);
encap_pogedgev(g->edges, seqlen + 2);
// estimate cap of g->rows
for(i=0;i<g->nodes->size;i++){
v = ref_pognodev(g->nodes, i);
v->roff = 0;
v->voff = 0;
v->coff = 0;
v->vst = 0;
v->aux = 0;
}
clear_u4v(g->stack);
push_u4v(g->stack, POG_HEAD_NODE);
rmax = 0;
bb = 1;
while(pop_u4v(g->stack, &nidx)){
u = ref_pognodev(g->nodes, nidx);
eidx = u->edge;
while(eidx){
e = ref_pogedgev(g->edges, eidx);
#if DEBUG
if(eidx == e->next){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
}
#endif
eidx = e->next;
v = ref_pognodev(g->nodes, e->node);
if(v->vst == 0){
bb ++;
if(bb > rmax){
rmax = bb;
}
}
v->vst ++;
if(v->vst == v->nin){
push_u4v(g->stack, e->node);
}
}
bb --;
}
#if DEBUG
if(bb){
fprintf(stderr, " -- something wrong in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
abort();
}
#endif
rmax += 2;
head_sl_b2v(g->rows, g->rows->n_head);
clear_and_encap_b2v(g->rows, rmax * seqinc + 8);
head_sr_b2v(g->rows, (16 - (((u8i)g->rows->buffer) & 0xF)) >> 1);
head_sl_b2v(g->btds, g->btds->n_head);
clear_and_encap_b2v(g->btds, rmax * seqinc + 8);
head_sr_b2v(g->btds, (16 - (((u8i)g->btds->buffer) & 0xF)) >> 1);
inc_b2v(g->rows, seqinc);
inc_b2v(g->btds, seqinc);
clear_u4v(g->rowr);
bb = 0;
for(i=0;i<g->nodes->size;i++){
v = ref_pognodev(g->nodes, i);
v->vst = 0;
v->erev = bb;
bb += v->nin;
if(i < 2) bb ++; // in case of add mnode
}
clear_u2v(g->btvs);
inc_u2v(g->btvs, 8);
clear_and_inc_u4v(g->btxs, bb + 1);
//g->btxs->buffer[0] = 0;
memset(g->btxs->buffer, 0, (bb + 1) * sizeof(u4i));
u = ref_pognodev(g->nodes, POG_HEAD_NODE);
if(g->rowr->size){
u->coff = u->roff = g->rowr->buffer[--g->rowr->size];
} else {
u->roff = g->rows->size;
inc_b2v(g->rows, seqinc);
u->coff = g->btds->size;
inc_b2v(g->btds, seqinc);
}
row = ref_b2v(g->rows, u->roff);
btds = ref_b2v(g->btds, u->coff);
if(g->par->alnmode == POG_ALNMODE_OVERLAP){ // overlap alignment
memset(row, 0, seqinc * sizeof(b2i));
//row[0] = g->par->T;
} else { // global
__m128i MIN;
MIN = _mm_set1_epi16(POG_SCORE_MIN);
for(j=0;j<slen;j++){
_mm_store_si128(((__m128i*)row) + j, MIN);
}
//row[0] = g->par->T;
}
memset(btds, 0, seqinc * sizeof(b2i));
if(g->par->near_dialog && g->par->W_score <= 0){
row[seqlex] = g->par->W;
row[seqlex + 1] = 0;
row[seqlex + 2] = num_min(Int(seqlex), 2 * g->par->W + 1);
} else {
row[seqlex] = 0;
row[seqlex + 1] = 0;
row[seqlex + 2] = seqlex;
}
}
// SSE
// BANDED, Auto fit the previous-row's max score in center
// OVERLAP
static inline void sse_band_row_rdaln_pog(POG *g, u4i nidx1, u4i nidx2, u4i seqlen, u2i vst, u4i coff1, u4i coff2, u4i roff1, u4i roff2, b2i *qp, int W, int center){
__m128i I, D, H, E, F, S, MAX, MIN, CMP;
__m128i BT, BT1, BT2, BT1_MASK, BT2_MASK, BTX_MASK;
b2i *row1, *row2, *btds;
u4i i, slen, seqlex, beg, end;
int lsth, lstf, msk, mi;
UNUSED(coff1);
slen = (seqlen + 7) / 8;
seqlex = slen * 8;
I = _mm_set1_epi16(g->par->I);
D = _mm_set1_epi16(g->par->D);
MIN = _mm_set1_epi16(POG_SCORE_MIN);
BT1_MASK = _mm_set1_epi16(0b10);
BT2_MASK = _mm_set1_epi16(0b01);
BTX_MASK = _mm_set1_epi16(vst << 2);
row1 = ref_b2v(g->rows, roff1);
row2 = ref_b2v(g->rows, roff2);
btds = ref_b2v(g->btds, coff2);
if(W){
if(center < 0){
if(row1[row1[seqlex]] >= g->par->W_score){
if(g->par->near_dialog){
if(row1[seqlex + 1] > 0 || row1[seqlex + 2] < Int(seqlex)){
if(row1[seqlex] == (row1[seqlex + 1] + row1[seqlex + 2]) / 2){
center = (row1[seqlex + 1] + row1[seqlex + 2]) / 2 + 1;
} else if(row1[seqlex] > (row1[seqlex + 1] + row1[seqlex + 2]) / 2){
center = (row1[seqlex + 1] + row1[seqlex + 2]) / 2 + 2;
} else {
center = (row1[seqlex + 1] + row1[seqlex + 2]) / 2;
}
} else { // first set center
center = row1[seqlex];
}
} else {
center = row1[seqlex];
}
beg = num_max(center - W, row1[seqlex + 1]);
end = num_min(center + 1 + W, row1[seqlex + 2] + 1);
if(end > seqlex) end = seqlex;
} else {
beg = row1[seqlex + 1];
end = num_min(row1[seqlex + 2] + 1, Int(seqlex));
}
} else {
beg = num_max(center - W, row1[seqlex + 1]);
end = num_min(center + 1 + W, row1[seqlex + 2] + 1);
if(end > seqlex) end = seqlex;
}
} else {
beg = 0;
end = seqlex;
}
if(beg & 0x7U) beg = beg & (~0x7U);
if(end & 0x7U) end = (end + 8) & (~0x7U);
beg = beg / 8;
end = (end + 7) / 8;
if(row1[seqlex + 1] >= row1[seqlex + 2]){ // happening in realign mode
for(i=beg*8;i<end*8;i+=8){
_mm_store_si128(((__m128i*)(row1 + i)), MIN);
}
} else {
if(Int(beg * 8) < row1[seqlex + 1]){
for(i=beg*8;Int(i)<row1[seqlex + 1];i+=8){
_mm_store_si128(((__m128i*)(row1 + i)), MIN);
}
}
if(Int(end * 8) > row1[seqlex + 2]){
for(i=row1[seqlex+2];i<end*8;i+=8){
_mm_store_si128(((__m128i*)(row1 + i)), MIN);
}
}
}
if(nidx2 == POG_TAIL_NODE){
while(end * 8 < seqlex){
_mm_store_si128(((__m128i*)(row1)) + end, MIN);
end ++;
}
}
MAX = _mm_set1_epi16(POG_SCORE_MIN);
if(beg){
lstf = lsth = POG_SCORE_MIN;
} else {
if(row1[seqlex + 1] >= row1[seqlex + 2]){
lstf = POG_SCORE_MIN;
lsth = 0; // auto global alignment
} else {
lstf = (g->par->alnmode == POG_ALNMODE_OVERLAP)? 0 : POG_SCORE_MIN;
if(nidx1){
lsth = (g->par->alnmode == POG_ALNMODE_OVERLAP)? 0 : POG_SCORE_MIN;;
} else {
lsth = g->par->T;
}
}
}
for(i=beg;i<end;i++){
E = _mm_load_si128(((__m128i*)(row1)) + i);
H = _mm_slli_si128(E, 2);
H = _mm_insert_epi16(H, lsth, 0);
H = _mm_adds_epi16(H, _mm_load_si128(((__m128i*)qp) + i));
lsth = _mm_extract_epi16(E, 7);
E = _mm_adds_epi16(E, D);
S = _mm_max_epi16(H, E);
BT1 = _mm_cmpgt_epi16(S, H);
BT1 = _mm_and_si128(BT1, BT1_MASK);
F = _mm_slli_si128(S, 2);
F = _mm_insert_epi16(F, lstf, 0);
F = _mm_adds_epi16(F, I);
F = _mm_max_epi16(S, F);
while(1){
H = _mm_slli_si128(F, 2);
H = _mm_insert_epi16(H, lstf, 0);
H = _mm_adds_epi16(H, I);
CMP = _mm_cmpgt_epi16(H, F);
msk = _mm_movemask_epi8(CMP);
if(msk == 0){
break;
} else {
F = _mm_max_epi16(H, F);
}
}
MAX = _mm_max_epi16(MAX, F);
lstf = _mm_extract_epi16(F, 7);
BT2 = _mm_cmpgt_epi16(F, S);
BT2 = _mm_and_si128(BT2, BT2_MASK);
BT = _mm_xor_si128(BT1, BT2); // (0, (1, 3), 2)
BT = _mm_xor_si128(BT, BTX_MASK); // (0, (1, 3), 2) | (vst << 2)
_mm_store_si128(((__m128i*)row2) + i, F);
_mm_stream_si128(((__m128i*)btds) + i, BT);
}
if(1){
b2i ary[8];
u4i j, k;
_mm_store_si128((__m128i*)ary, MAX);
k = 0;
for(j=1;j<8;j++){
if(ary[j] > ary[k]){
k = j;
}
}
mi = beg * 8 + k;
for(i=beg+1;i<end;i++){
if(row2[i * 8 + k] > row2[mi]){
mi = i * 8 + k;
}
}
} else {
mi = beg * 8;
for(i=mi+1;i<end*8;i++){
if(row2[i] > row2[mi]){
mi = i;
}
}
}
row2[seqlex] = mi;
row2[seqlex + 1] = beg * 8;
row2[seqlex + 2] = end * 8;
}
static inline void merge_row_rdaln_pog(POG *g, u4i seqlen, u4i coff1, u4i coff2, u4i roff1, u4i roff2){
b2i *row1, *row2, *btd1, *btd2;
u4i i, seqlex, beg[3], end[3], sz, b;
row1 = ref_b2v(g->rows, roff1);
row2 = ref_b2v(g->rows, roff2);
btd1 = ref_b2v(g->btds, coff1);
btd2 = ref_b2v(g->btds, coff2);
seqlex = roundup_times(seqlen, 8);
beg[0] = (row1[seqlex + 1]);
beg[1] = (row2[seqlex + 1]);
end[0] = (row1[seqlex + 2]);
end[1] = (row2[seqlex + 2]);
beg[2] = num_max(beg[0], beg[1]);
end[2] = num_min(end[0], end[1]);
if(1){
__m128i R1, R2, D1, D2, MK;
for(i=beg[2];i&0x7;i++){
if(row2[i] < row1[i]){
row2[i] = row1[i];
btd2[i] = btd1[i];
}
}
for(;i+8<=end[2];i+=8){
R1 = _mm_load_si128((__m128i*)(row1 + i));
R2 = _mm_load_si128((__m128i*)(row2 + i));
D1 = _mm_load_si128((__m128i*)(btd1 + i));
D2 = _mm_load_si128((__m128i*)(btd2 + i));
MK = _mm_cmpgt_epi16(R1, R2);
R2 = _mm_max_epi16(R1, R2);
_mm_store_si128((__m128i*)(row2 + i), R2);
D2 = _mm_or_si128(_mm_and_si128(MK, D1), _mm_andnot_si128(MK, D2));
_mm_store_si128((__m128i*)(btd2 + i), D2);
}
for(;i<end[2];i++){
if(row2[i] < row1[i]){
row2[i] = row1[i];
btd2[i] = btd1[i];
}
}
} else {
for(i=beg[2];i<end[2];i++){
if(row2[i] < row1[i]){
row2[i] = row1[i];
btd2[i] = btd1[i];
}
}
}
if(0){
if(beg[0] < beg[2]){
sz = num_min(beg[2], end[0]) - beg[0];
memcpy(row2 + beg[0], row1 + beg[0], sz * sizeof(b2i));
memcpy(btd2 + beg[0], btd1 + beg[0], sz * sizeof(b2i));
}
for(i=end[2];i<beg[2];i++){ // in case of two independent regions
row2[i] = POG_SCORE_MIN;
}
if(end[0] > end[2]){
sz = num_min(end[0], seqlex) - end[2];
memcpy(row2 + end[2], row1 + end[2], sz * sizeof(b2i));
memcpy(btd2 + end[2], btd1 + end[2], sz * sizeof(b2i));
}
} else {
if(beg[0] < beg[1]){
b = beg[0];
if(end[0] >= beg[1]){
sz = beg[1] - beg[0];
memcpy(row2 + b, row1 + b, sz * sizeof(b2i));
memcpy(btd2 + b, btd1 + b, sz * sizeof(b2i));
} else {
__m128i F;
F = _mm_set1_epi16(POG_SCORE_MIN);
sz = end[0] - beg[0];
memcpy(row2 + b, row1 + b, sz * sizeof(b2i));
memcpy(btd2 + b, btd1 + b, sz * sizeof(b2i));
for(i=end[0];i<beg[1];i+=8){
_mm_store_si128(((__m128i*)(row2 + i)), F);
}
}
}
if(end[0] > end[1]){
if(beg[0] <= end[1]){
b = end[1];
sz = end[0] - b;
memcpy(row2 + b, row1 + b, sz * sizeof(b2i));
memcpy(btd2 + b, btd1 + b, sz * sizeof(b2i));
} else {
__m128i F;
F = _mm_set1_epi16(POG_SCORE_MIN);
b = beg[0];
sz = end[0] - b;
memcpy(row2 + b, row1 + b, sz * sizeof(b2i));
memcpy(btd2 + b, btd1 + b, sz * sizeof(b2i));
for(i=end[1];i<beg[0];i+=8){
_mm_store_si128(((__m128i*)(row2 + i)), F);
}
}
}
}
row2[seqlex + 1] = num_min(beg[0], beg[1]);
row2[seqlex + 2] = num_max(end[0], end[1]);
if(row1[(row1[seqlex])] > row2[(row2[seqlex])]){
row2[seqlex] = row1[seqlex];
}
}
static inline void set_rd_query_prof(POG *g, u4i rid){
b2i *qp;
u4i seqoff, seqlen, seqlex, slen, seqinc;
u4i i, j, bb, bk;
seqoff = g->seqs->rdoffs->buffer[rid];
seqlen = g->seqs->rdlens->buffer[rid];
seqlex = roundup_times(seqlen, 8);
slen = seqlex >> 3;
seqinc = seqlex + 8;
head_sl_b2v(g->qprof, g->qprof->n_head);
if(g->par->tribase){
clear_and_encap_b2v(g->qprof, seqlex * (POG_BASEMAX + 2) + 8);
head_sr_b2v(g->qprof, (16 - (((u8i)g->qprof->buffer) & 0xF)) >> 1);
for(i=0;i<=POG_BASEMAX;i++){
qp = g->qprof->buffer + i * seqlex;
bk = 0;
for(j=0;j<seqlen;j++){
bb = get_basebank(g->seqs->rdseqs, seqoff + j);
bk = ((bk << 2) | bb) & POG_BASEMAX;
if(bb == (i & 0x03)){
if(bk == i){
qp[j] = g->par->M + g->par->tribase;
} else {
qp[j] = g->par->M;
}
} else {
qp[j] = g->par->X;
}
}
for(;j<seqlex;j++){
qp[j] = POG_SCORE_MIN;
}
}
} else {
clear_and_encap_b2v(g->qprof, seqlex * (4 + 1) + 8);
head_sr_b2v(g->qprof, (16 - (((u8i)g->qprof->buffer) & 0xF)) >> 1);
for(i=0;i<4;i++){
qp = g->qprof->buffer + i * seqlex;
for(j=0;j<seqlen;j++){
bb = get_basebank(g->seqs->rdseqs, seqoff + j);
if(bb == (i & 0x03)){
qp[j] = g->par->M;
} else {
qp[j] = g->par->X;
}
}
for(;j<seqlex;j++){
qp[j] = POG_SCORE_MIN;
}
}
}
{
__m128i X;
qp = g->qprof->buffer + i * seqlex;
X = _mm_set1_epi16(g->par->X);
for(j=0;j<slen;j++){