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kswx.h
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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/>.
*/
#ifndef __KSW_EXT_RJ_H
#define __KSW_EXT_RJ_H
#include "ksw.h"
#include "dna.h"
#include "string.h"
#include "list.h"
#include <math.h>
#include <float.h>
typedef struct {
int score;
int tb, te, qb, qe;
int aln, mat, mis, ins, del;
} kswx_t;
static const kswr_t KSWR_NULL = (kswr_t){0, 0, 0, 0, 0, 0, 0};
static const kswx_t KSWX_NULL = (kswx_t){0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
static inline void kswx_push_cigar(u32list *cigars, uint32_t op, uint32_t len){
if(len == 0) return;
if(cigars->size && (cigars->buffer[cigars->size-1] & 0xF) == op){
cigars->buffer[cigars->size-1] += len << 4;
} else push_u32list(cigars, (len << 4) | op);
}
static inline void kswx_push_cigars(u32list *cigars, uint32_t *cigar, size_t size){
if(size == 0) return;
if(cigars->size && (cigars->buffer[cigars->size-1] & 0x0F) == (cigar[0] & 0x0FU)){
cigars->buffer[cigars->size-1] += cigar[0] & 0xFFFFFFF0U;
append_array_u32list(cigars, cigar + 1, size - 1);
} else append_array_u32list(cigars, cigar, size);
}
static inline void kswx_print_cigars(uint32_t *cigar, size_t size, FILE *out){
size_t i;
uint32_t op, len;
for(i=0;i<size;i++){
op = cigar[i] & 0x0F;
len = cigar[i] >> 4;
fprintf(out, "%d%c", len, "MIDX"[op]);
}
fflush(out);
}
static inline kswx_t kswx_stat_cigars(uint32_t *cigar, size_t size){
kswx_t x;
size_t i;
uint32_t op, len;
x = KSWX_NULL;
for(i=0;i<size;i++){
op = cigar[i] & 0x0F;
len = cigar[i] >> 4;
x.aln += len;
switch(op){
case 0: x.mat += len; x.te += len; x.qe += len; break;
case 1: x.ins += len; x.qe += len; break;
case 2: x.del += len; x.te += len; break;
}
}
return x;
}
static inline void revseq_bytes(uint8_t *ary, int size){
int i, v;
for(i=0;i<size>>1;i++){
v = ary[i]; ary[i] = ary[size - 1 - i]; ary[size - 1 - i] = v;
}
}
static inline void revseq_4bytes(uint32_t *ary, int size){
int i;
uint32_t v;
for(i=0;i<size>>1;i++){
v = ary[i]; ary[i] = ary[size - 1 - i]; ary[size - 1 - i] = v;
}
}
#define kswx_roundup8x(n) (((n) + 0x7LLU) & 0xFFFFFFFFFFFFFFF8LLU)
// diagonal will shift 1 bp to max score of each row
static inline kswx_t kswx_extend_align_shift_core(int qlen, uint8_t *query, int tlen, uint8_t *target, int strand, int init_score, int W, int M, int X, int I, int D, int E, int T, u8list *mem_cache, u32list *cigars){
kswx_t x;
int *rh, *re, *zb;
uint8_t *z, *zi;
int8_t *qp, *qpp;
register uint8_t d;
int ql, tl, n_col;
int i, j, jb, je, h1, c;
register int h, m, e, f, t;
int max_gap, max, mi, mj, imax, mj2, gmax, gi, gj;
clear_u32list(cigars);
x = KSWX_NULL;
if(init_score < 0) init_score = 0;
if(qlen <= 0 || tlen <= 0){ x.score = init_score; return x; }
if(W > 0){
max = ((qlen < tlen)? qlen : tlen) * M + init_score + (- T);
max_gap = (max + (((I > D)? I : D))) / (- E) + 1;
if(max_gap < 1) max_gap = 1;
if(W > max_gap) W = max_gap;
} else W = -W;
W = num_min(W, num_max(qlen, tlen));
if(qlen < tlen){
if(qlen + W < tlen){ ql = qlen; tl = qlen + W; }
else { ql = qlen; tl = tlen; }
} else {
if(tlen + W < qlen){ tl = tlen; ql = tlen + W; }
else { tl = tlen; ql = qlen; }
}
n_col = tl < 2 * W + 1? tl : 2 * W + 1;
encap_u8list(mem_cache, kswx_roundup8x(mem_cache->size) - mem_cache->size
+ kswx_roundup8x((tl + 2) * sizeof(int)) * 2
+ kswx_roundup8x((ql + 2) * sizeof(int))
+ kswx_roundup8x(((long long)ql) * n_col)
+ kswx_roundup8x(tl + 2) * sizeof(int8_t) * 4); // assume only A,C,G,T
rh = (int*)(mem_cache->buffer + kswx_roundup8x(mem_cache->size));
re = (int*)(mem_cache->buffer + kswx_roundup8x(mem_cache->size) + kswx_roundup8x((tl + 2) * sizeof(int)));
zb = (int*)(mem_cache->buffer + kswx_roundup8x(mem_cache->size) + kswx_roundup8x((tl + 2) * sizeof(int)) * 2);
z = (mem_cache->buffer + kswx_roundup8x(mem_cache->size) + kswx_roundup8x((tl + 2) * sizeof(int)) * 2 + kswx_roundup8x((ql + 2) * sizeof(int)));
qp = (int8_t*)(mem_cache->buffer + kswx_roundup8x(mem_cache->size) + kswx_roundup8x((tl + 2) * sizeof(int)) * 2 + kswx_roundup8x((ql + 2) * sizeof(int)) + kswx_roundup8x(((long long)ql) * n_col));
for(c=i=0;c<4;c++){
for(j=0;j<tl;j++) qp[i++] = (c == target[j * strand])? M : X;
}
rh[0] = init_score; rh[1] = init_score + D + E;
for(j=2;j<=tl;j++) rh[j] = rh[j - 1] + E;
for(j=0;j<=tl;j++) re[j] = -10000;
max = init_score; mi = -1; mj = -1; gmax = 0; gi = -1; gj = -1;
jb = 0; je = tl;
for(i=c=0;i<ql;i++){
if(jb < c - W) jb = c - W;
if(je > c + W + 1) je = c + W + 1;
if(je > tl) je = tl;
if(jb == 0) h1 = init_score + I + E * (i + 1);
else h1 = -10000;
zi = z + (i * n_col);
zb[i] = jb;
imax = 0; mj2 = -1; f = -10000;
qpp = qp + query[i * strand] * tl;
for(j=jb;j<je;j++){
//m = rh[j] + ((query[i * strand] == target[j * strand])? M : X);
m = rh[j] + qpp[j];
rh[j] = h1;
e = re[j];
if(m >= e){ d = 0; h = m; }
else { d = 1; h = e; }
if(h < f){ d = 2; h = f; }
h1 = h;
if(h > imax){ imax = h; mj2 = j; }
t = m + I + E;
e = e + E;
if(e > t){ d |= 1 << 2; }
else { e = t; }
re[j] = e;
t = m + D + E;
f = f + E;
if(f > t){ d |= 2 << 4; }
else { f = t; }
zi[j-jb] = d;
}
rh[j] = h1; re[j] = -10000;
if(j == tlen && gmax < h1){ gmax = h1; gi = i; gj = j - 1; }
if(i + 1 == qlen && gmax < imax){ gmax = imax; gi = i; gj = mj2; }
if(imax > max){
max = imax; mi = i; mj = mj2;
} else if(imax <= 0) break;
c ++;
if(c < mj2){
c ++;
if(je < tl){
rh[je + 1] = -10000;
re[je + 1] = -10000;
}
} else if(c > mj2) {
c --;
if(jb){
rh[jb-1] = -10000;
re[jb-1] = -10000;
}
}
jb = 0; je = tl;
}
if(gmax > 0 && gmax >= max + T){
x.score = gmax; x.qe = gi; x.te = gj;
} else {
x.score = max; x.qe = mi; x.te = mj;
}
i = x.qe; j = x.te;
d = 0;
while(i >= 0 && j >= 0){
d = (z[i * n_col + (j - zb[i])] >> (d << 1)) & 0x03;
if(d == 0){
if(query[i * strand] == target[j * strand]){ x.mat ++; } else { x.mis ++; } i --; j --;
} else if(d == 1){
i --; x.ins ++;
} else {
j --; x.del ++;
}
if(cigars) kswx_push_cigar(cigars, d, 1);
}
if(i >= 0){
x.ins += i + 1;
if(cigars) kswx_push_cigar(cigars, 1, i + 1);
}
if(j >= 0){
x.del += j + 1;
if(cigars) kswx_push_cigar(cigars, 2, j + 1);
}
if(cigars) reverse_u32list(cigars);
x.aln = x.mat + x.mis + x.ins + x.del;
x.qe ++; x.te ++;
return x;
}
static inline kswx_t kswx_extend_align_core(int qlen, uint8_t *query, int tlen, uint8_t *target, int strand, int init_score, int W, int M, int X, int I, int D, int E, int T, u8list *mem_cache, u32list *cigars){
kswx_t x;
int *rh, *re;
uint8_t *z, *zi, d;
int ql, tl, n_col;
int i, j, jb, je, h1, h, m, e, f, t;
int max_gap, max, mi, mj, imax, mj2, gmax, gi, gj;
x = KSWX_NULL;
if(init_score < 0) init_score = 0;
if(qlen <= 0 || tlen <= 0){ x.score = init_score; return x; }
if(W > 0){
max = ((qlen < tlen)? qlen : tlen) * M + init_score + (- T);
max_gap = (max + (((I > D)? I : D))) / (- E) + 1;
if(max_gap < 1) max_gap = 1;
if(W > max_gap) W = max_gap;
} else W = -W;
W = num_min(W, num_max(qlen, tlen));
if(qlen < tlen){
if(qlen + W < tlen){ ql = qlen; tl = qlen + W; }
else { ql = qlen; tl = tlen; }
} else {
if(tlen + W < qlen){ tl = tlen; ql = tlen + W; }
else { tl = tlen; ql = qlen; }
}
n_col = tl < 2 * W + 1? tl : 2 * W + 1;
encap_u8list(mem_cache, kswx_roundup8x((tl + 2) * sizeof(int)) + kswx_roundup8x((tl + 2) * sizeof(int)) + kswx_roundup8x(((long long)ql) * n_col));
rh = (int*)(mem_cache->buffer + mem_cache->size);
re = (int*)(mem_cache->buffer + mem_cache->size + kswx_roundup8x((tl + 2) * sizeof(int)));
z = (mem_cache->buffer + mem_cache->size + kswx_roundup8x((tl + 2) * sizeof(int)) + kswx_roundup8x((tl + 2) * sizeof(int)));
rh[0] = init_score; rh[1] = init_score + D + E;
for(j=2;j<=tl;j++) rh[j] = rh[j - 1] + E;
for(j=0;j<=tl;j++) re[j] = -10000;
max = init_score; mi = -1; mj = -1; gmax = 0; gi = -1; gj = -1;
jb = 0; je = tl;
for(i=0;i<ql;i++){
jb = i - W; if(jb < 0) jb = 0;
je = i + W + 1; if(je > tl) je = tl;
if(jb == 0) h1 = init_score + I + E * (i + 1);
else h1 = -10000;
zi = &z[i * n_col];
imax = 0; mj2 = -1; f = -10000;
for(j=jb;j<je;j++){
m = rh[j] + ((query[i * strand] == target[j * strand])? M : X);
rh[j] = h1;
e = re[j];
d = m >= e? 0 : 1;
h = m >= e? m : e;
d = h >= f? d : 2;
h = h >= f? h : f;
h1 = h;
imax = imax > h? imax : h;
mj2 = imax > h? mj2 : j;
t = m + I + E;
e = e + E;
d |= e > t? 1<<2 : 0;
e = e > t? e : t;
re[j] = e;
t = m + D + E;
f = f + E;
d |= f > t? 2<<4 : 0;
f = f > t? f : t;
zi[j-jb] = d;
}
rh[j] = h1; re[j] = -10000;
if(j == tlen && gmax < h1){ gmax = h1; gi = i; gj = j - 1; }
if(i + 1 == qlen && gmax < imax){ gmax = imax; gi = i; gj = mj2; }
if(imax > max){
max = imax; mi = i; mj = mj2;
} else if(imax <= 0) break;
}
if(gmax > 0 && gmax >= max + T){
x.score = gmax; x.qe = gi; x.te = gj;
} else {
x.score = max; x.qe = mi; x.te = mj;
}
i = x.qe; j = x.te;
d = 0;
clear_u32list(cigars);
while(i >= 0 && j >= 0){
d = (z[i * n_col + j - (i > W? i - W : 0)] >> (d << 1)) & 0x03;
if(d == 0){
if(query[i * strand] == target[j * strand]){ x.mat ++; } else { x.mis ++; } i --; j --;
} else if(d == 1){
i --; x.ins ++;
} else {
j --; x.del ++;
}
if(cigars) kswx_push_cigar(cigars, d, 1);
}
if(i >= 0){
x.ins += i + 1;
if(cigars) kswx_push_cigar(cigars, 1, i + 1);
}
if(j >= 0){
x.del += j + 1;
if(cigars) kswx_push_cigar(cigars, 2, j + 1);
}
if(cigars) reverse_u32list(cigars);
x.aln = x.mat + x.mis + x.ins + x.del;
x.qe ++; x.te ++;
return x;
}
static inline kswx_t kswx_mismatch_free_extend_align_core(int qlen, uint8_t *query, int tlen, uint8_t *target, int strand, int init_score, int W, int M, int I, int D, int E, int T, u8list *mem_cache, u32list *cigars){
kswx_t x;
int *rh, *re;
uint8_t *z, *zi, d;
int ql, tl, n_col;
int i, j, jb, je, h1, h, m, e, f;
int max_gap, max, mi, mj, imax, mj2, gmax, gi, gj;
x = KSWX_NULL;
if(init_score < 0) init_score = 0;
if(qlen <= 0 || tlen <= 0){ x.score = init_score; return x; }
if(W > 0){
max = ((qlen < tlen)? qlen : tlen) * M + init_score + (- T);
max_gap = (max + (((I > D)? I : D))) / (- E) + 1;
if(max_gap < 1) max_gap = 1;
if(W > max_gap) W = max_gap;
} else W = -W;
W = num_min(W, num_max(qlen, tlen));
if(qlen < tlen){
if(qlen + W < tlen){ ql = qlen; tl = qlen + W; }
else { ql = qlen; tl = tlen; }
} else {
if(tlen + W < qlen){ tl = tlen; ql = tlen + W; }
else { tl = tlen; ql = qlen; }
}
n_col = tl < 2 * W + 1? tl : 2 * W + 1;
encap_u8list(mem_cache, kswx_roundup8x((tl + 2) * sizeof(int)) + kswx_roundup8x((tl + 2) * sizeof(int)) + kswx_roundup8x(((long long)ql) * n_col));
rh = (int*)(mem_cache->buffer + mem_cache->size);
re = (int*)(mem_cache->buffer + mem_cache->size + kswx_roundup8x((tl + 2) * sizeof(int)));
z = (mem_cache->buffer + mem_cache->size + kswx_roundup8x((tl + 2) * sizeof(int)) + kswx_roundup8x((tl + 2) * sizeof(int)));
rh[0] = init_score; rh[1] = init_score + D + E;
for(j=2;j<=tl;j++) rh[j] = rh[j - 1] + E;
for(j=0;j<=tl;j++) re[j] = -10000;
max = init_score; mi = -1; mj = -1; gmax = 0; gi = -1; gj = -1;
jb = 0; je = tl;
for(i=0;i<ql;i++){
jb = i - W; if(jb < 0) jb = 0;
je = i + W + 1; if(je > tl) je = tl;
if(jb == 0) h1 = init_score + I + E * (i + 1);
else h1 = -10000;
zi = &z[i * n_col];
imax = 0; mj2 = -1; f = h1 + D + E;
for(j=jb;j<je;j++){
e = re[j];
if(query[i * strand] == target[j * strand]){
m = rh[j] + M;
rh[j] = h1;
if(m >= e){
if(m >= f){
d = 0;
h = m;
f = m + D + E;
e = m + I + E;
} else {
d = 2;
h = f;
f = f + E;
e = f + I + E;
}
} else {
if(e >= f){
d = 1;
h = e;
f = e + D + E;
e = e + E;
} else {
d = 2;
h = f;
f = f + E;
e = f + I + E;
}
}
} else {
rh[j] = h1;
{
if(e >= f){
d = 1;
h = e;
f = e + D + E;
e = e + E;
} else {
d = 2;
h = f;
f = f + E;
e = f + I + E;
}
}
}
h1 = h;
if(imax < h){ imax = h; mj2 = j; }
re[j] = e;
zi[j-jb] = d;
}
rh[j] = h1; re[j] = -10000;
if(j == tlen && gmax < h1){ gmax = h1; gi = i; gj = j - 1; }
if(i + 1 == qlen && gmax < imax){ gmax = imax; gi = i; gj = mj2; }
if(imax > max){
max = imax; mi = i; mj = mj2;
} else if(imax <= 0) break;
}
if(gmax > 0 && gmax >= max + T){
x.score = gmax; x.qe = gi; x.te = gj;
} else {
x.score = max; x.qe = mi; x.te = mj;
}
i = x.qe; j = x.te;
d = 0;
clear_u32list(cigars);
while(i >= 0 && j >= 0){
d = (z[i * n_col + j - (i > W? i - W : 0)]) & 0x03;
if(d == 0){
x.mat ++; i --; j --;
} else if(d == 1){
i --; x.ins ++;
} else {
j --; x.del ++;
}
if(cigars) kswx_push_cigar(cigars, d, 1);
}
if(i >= 0){
x.ins += i + 1;
if(cigars) kswx_push_cigar(cigars, 1, i + 1);
}
if(j >= 0){
x.del += j + 1;
if(cigars) kswx_push_cigar(cigars, 2, j + 1);
}
if(cigars) reverse_u32list(cigars);
x.aln = x.mat + x.mis + x.ins + x.del;
x.qe ++; x.te ++;
return x;
}
static inline kswx_t kswx_extend_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int strand, int init_score, int W, int M, int X, int I, int D, int E, int T, int *n_cigar, uint32_t **cigar){
u8list *caches;
u32list *cigars;
kswx_t x;
caches = init_u8list(256);
cigars = init_u32list(64);
x = kswx_extend_align_shift_core(qlen, query, tlen, target, strand, init_score, W, M, X, I, D, E, T, caches, cigars);
free_u8list(caches);
*n_cigar = cigars->size;
*cigar = cigars->buffer;
free(cigars);
return x;
}
static inline kswx_t kswx_refine_alignment(uint8_t *query, int qb, uint8_t *target, int tb, int W, int M, int X, int I, int D, int E, u32list *cigars, u8list *mem_cache, u32list *cigars2){
kswx_t y;
int *rh, *re;
int *zb, *ze, *zw;
int ql, tl, _zb, _ze, tx, qx;
int qe, te;
uint8_t *z, *zi;
int8_t *qp, *qpp;
register uint8_t d;
register int h, m, e, f, t;
long long i, j;
int op, len, h1, c;
clear_u32list(cigars2);
qe = qb; te = tb;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0: qe += len; te += len; break;
case 1: qe += len; break;
default: te += len;
}
}
ql = qe - qb;
tl = te - tb;
if(ql == 0 || tl == 0) return KSWX_NULL;
clear_and_encap_u8list(mem_cache,
kswx_roundup8x((tl + 2) * sizeof(int)) * 2 // rh, re
+ kswx_roundup8x((ql + 2) * sizeof(int)) * 3 // zb, ze, zw
+ kswx_roundup8x(((long long)ql) * tl) // z
+ kswx_roundup8x(tl + 2) * sizeof(int8_t) * 4); // qp
rh = (int*)(mem_cache->buffer);
re = (int*)(((void*)rh) + kswx_roundup8x((tl + 2) * sizeof(int)));
zb = (int*)(((void*)re) + kswx_roundup8x((tl + 2) * sizeof(int)));
ze = (int*)(((void*)zb) + kswx_roundup8x((ql + 2) * sizeof(int)));
zw = (int*)(((void*)ze) + kswx_roundup8x((ql + 2) * sizeof(int)));
z = (uint8_t*)(((void*)zw) + kswx_roundup8x((ql + 2) * sizeof(int)));
qp = (int8_t*)(((void*)z) + kswx_roundup8x(((long long)ql) * tl));
for(c=i=0;c<4;c++){
for(j=0;j<tl;j++) qp[i++] = (c == target[j + tb])? M : X;
}
// calculate alignment band
// basic band
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
for(j=0;j<len;j++) zw[qx++] = W;
break;
case 1:
for(j=0;j<len;j++) zw[qx++] = W + len;
break;
default:
zw[qx] += len;
}
}
// extending bandwidth around indels
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
qx += len;
break;
case 1:
for(j=1;j<len&&j<qx;j++) zw[qx-j] += len - j;
qx += len - 1;
for(j=1;j<len&&j+qx<ql;j++) zw[qx+j] += len - j;
qx ++;
break;
default:
for(j=1;j<len&&j<qx;j++) zw[qx-j] += len - j;
for(j=1;j<len&&j+qx<ql;j++) zw[qx+j] += len - j;
}
}
// generate band region
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
for(j=0;j<len;j++){
_zb = tx - zw[qx]; if(_zb < 0) _zb = 0;
_ze = tx + 1 + zw[qx]; if(_ze > tl) _ze = tl;
zb[qx] = _zb;
ze[qx] = _ze;
tx ++;
qx ++;
}
break;
case 1:
for(j=0;j<len;j++){
_zb = tx - zw[qx]; if(_zb < 0) _zb = 0;
_ze = tx + 1 + zw[qx]; if(_ze > tl) _ze = tl;
zb[qx] = _zb;
ze[qx] = _ze;
qx ++;
}
break;
default:
tx += len;
}
}
// trim band beg
_zb = 0;
for(i=0;i<ql;i++){
if(zb[i] < _zb) zb[i] = _zb;
else if(zb[i] > _zb) _zb = zb[i];
}
// trim band end
_ze = tl;
for(i=ql-1;i>=0;i--){
if(ze[i] > _ze) ze[i] = _ze;
else if(ze[i] < _ze) _ze = ze[i];
}
// perform alignment
rh[0] = 0;
for(i=1;i<=tl;i++) rh[i] = -10000;
for(i=0;i<=tl;i++) re[i] = -10000;
for(i=0;i<ql;i++){
qpp = qp + query[i + qb] * tl;
h1 = f = -10000;
zi = z + (((long long)i) * tl);
//fprintf(stdout, "ZW\t%d\t%d\t%d\t%d\n", (int)i, zb[i], ze[i], ze[i] - zb[i]);
for(j=zb[i];j<ze[i];j++){
m = rh[j] + qpp[j];
rh[j] = h1;
e = re[j];
if(m >= e){ d = 0; h = m; }
else { d = 1; h = e; }
if(h < f){ d = 2; h = f; }
h1 = h;
t = m + I + E;
e = e + E;
if(e > t){ d |= 1 << 2; }
else { e = t; }
re[j] = e;
t = m + D + E;
f = f + E;
if(f > t){ d |= 2 << 4; }
else { f = t; }
zi[j-zb[i]] = d;
}
rh[j] = h1; re[j] = -10000;
}
y.qb = qb; y.qe = qe; y.tb = tb; y.te = te;
y.score = rh[tl];
y.mat = y.mis = y.ins = y.del = y.aln = 0;
d = 0;
i = ql - 1; j = tl - 1;
while(i >= 0 && j >= 0){
d = (z[i * tl + (j - zb[i])] >> (d << 1)) & 0x03;
if(d == 0){
if(query[i + y.qb] == target[j + y.tb]){ y.mat ++; } else { y.mis ++; } i --; j --;
} else if(d == 1){
i --; y.ins ++;
} else {
j --; y.del ++;
}
kswx_push_cigar(cigars2, d, 1);
}
if(i >= 0){
y.ins += i + 1;
kswx_push_cigar(cigars2, 1, i + 1);
}
if(j >= 0){
y.del += j + 1;
kswx_push_cigar(cigars2, 2, j + 1);
}
reverse_u32list(cigars2);
y.aln = y.mat + y.mis + y.ins + y.del;
return y;
}
// qvs: 0:errQV, 1:misQV, 2:insQV, 3:delQV, 4:mrgQV, 5, misTag, 6, delTag
static inline kswx_t kswx_refine_alignment_5q(uint8_t *query, int qb, uint8_t *target, int tb, int W, uint8_t QCLP, uint8_t QMIS, uint8_t QDEL, uint8_t *qvs[7], u32list *cigars, u8list *mem_cache, u32list *cigars2){
kswx_t y;
uint32_t *rh, SCORE_INF;
int *zb, *ze, *zw;
int ql, tl, rl, _zb, _ze, tx, qx;
int qe, te;
uint8_t *z, *zi;
uint8_t d, qmat[4], qins, qdel[4];
register uint32_t h1, h, m, e, f;
long long i, j;
int op, len;
SCORE_INF = 0xFFFFFFFFU >> 1;
clear_u32list(cigars2);
qe = qb; te = tb;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0: qe += len; te += len; break;
case 1: qe += len; break;
default: te += len;
}
}
ql = qe - qb;
tl = te - tb;
if(ql == 0 || tl == 0) return KSWX_NULL;
rl = tl;
clear_and_encap_u8list(mem_cache,
kswx_roundup8x((tl + 2) * sizeof(uint32_t)) // rh
+ kswx_roundup8x((ql + 2) * sizeof(int)) * 3 // zb, ze, zw
+ kswx_roundup8x(((long long)ql) * rl)); // z
rh = (uint32_t*)(mem_cache->buffer);
zb = (int*)(((void*)rh) + kswx_roundup8x((tl + 2) * sizeof(uint32_t)));
ze = (int*)(((void*)zb) + kswx_roundup8x((ql + 2) * sizeof(int)));
zw = (int*)(((void*)ze) + kswx_roundup8x((ql + 2) * sizeof(int)));
z = (uint8_t*)(((void*)zw) + kswx_roundup8x((ql + 2) * sizeof(int)));
// calculate alignment band
// basic band
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
for(j=0;j<len;j++) zw[qx++] = W;
break;
case 1:
for(j=0;j<len;j++) zw[qx++] = W + len;
break;
default:
zw[qx] += len;
}
}
// extending bandwidth around indels
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
qx += len;
break;
case 1:
for(j=1;j<len&&j<qx;j++) zw[qx-j] += len - j;
qx += len - 1;
for(j=1;j<len&&j+qx<ql;j++) zw[qx+j] += len - j;
qx ++;
break;
default:
for(j=1;j<len&&j<qx;j++) zw[qx-j] += len - j;
for(j=1;j<len&&j+qx<ql;j++) zw[qx+j] += len - j;
}
}
// generate band region
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
for(j=0;j<len;j++){
_zb = tx - zw[qx]; if(_zb < 0) _zb = 0;
_ze = tx + 1 + zw[qx]; if(_ze > tl) _ze = tl;
zb[qx] = _zb;
ze[qx] = _ze;
tx ++;
qx ++;
}
break;
case 1:
for(j=0;j<len;j++){
_zb = tx - zw[qx]; if(_zb < 0) _zb = 0;
_ze = tx + 1 + zw[qx]; if(_ze > tl) _ze = tl;
zb[qx] = _zb;
ze[qx] = _ze;
qx ++;
}
break;
default:
tx += len;
}
}
// trim band beg
_zb = 0;
for(i=0;i<ql;i++){
if(zb[i] < _zb) zb[i] = _zb;
else if(zb[i] > _zb) _zb = zb[i];
}
// trim band end
_ze = tl;
for(i=ql-1;i>=0;i--){
if(ze[i] > _ze) ze[i] = _ze;
else if(ze[i] < _ze) _ze = ze[i];
}
// perform alignment
for(i=0;i<=tl;i++) rh[i] = SCORE_INF;
for(i=0;i<ql;i++){
if(i == 0){
h1 = i * QCLP;
f = (i + 1) * QCLP;
} else {
h1 = f = SCORE_INF;
}
zi = z + (i * rl);
for(j=0;j<4;j++){
if(j == query[i + qb]) qmat[j] = 0;
else if(j == qvs[5][i + qb]) qmat[j] = qvs[1][i + qb];
else qmat[j] = QMIS;
}
qins = qvs[2][i + qb];
if(i + 1 == ql) qdel[0] = qdel[1] = qdel[2] = qdel[3] = QCLP;
else {
for(j=0;j<4;j++){
if(j == qvs[6][i + 1 + qb]){
qdel[j] = qvs[3][i + 1 + qb];
} else qdel[j] = QDEL;
}
}
for(j=zb[i];j<ze[i];j++){
m = h1 + qmat[target[j + tb]];
f = f + qdel[target[j + tb]];
if(m <= f){ d = 0; h = m; }
else { d = 2; h = f; }
e = rh[j] + qins;
if(e < h){ d = 1; h = e; }
h1 = rh[j];
rh[j] = f = h;
zi[j-zb[i]] = d;
}
}
y.qb = qb; y.qe = qe; y.tb = tb; y.te = te;
y.score = - (int)rh[tl-1];
y.mat = y.mis = y.ins = y.del = y.aln = 0;
d = 0;
i = ql - 1; j = tl - 1;
//String *qs = init_string(1024);
//String *ts = init_string(1024);
//String *ms = init_string(1024);
while(i >= 0 && j >= 0){
d = z[i * rl + (j - zb[i])] & 0x03;
if(d == 0){
//add_char_string(qs, bit_base_table[query[i + y.qb]]);
//add_char_string(ts, bit_base_table[target[j + y.tb]]);
if(query[i + y.qb] == target[j + y.tb]){
//add_char_string(ms, '|');
y.mat ++;
} else {
//add_char_string(ms, '*');
y.mis ++;
}
i --; j --;
} else if(d == 1){
//add_char_string(qs, bit_base_table[query[i + y.qb]]);
//add_char_string(ts, '-');
//add_char_string(ms, '-');
i --; y.ins ++;
} else {
//add_char_string(qs, '-');
//add_char_string(ts, bit_base_table[target[j + y.tb]]);
//add_char_string(ms, '-');
j --; y.del ++;
}
kswx_push_cigar(cigars2, d, 1);
}
//reverse_string(qs);
//reverse_string(ts);
//reverse_string(ms);
//printf("%s\n%s\n%s\n", qs->string, ms->string, ts->string);
//free_string(qs);
//free_string(ts);
//free_string(ms);
if(1){
if(i >= 0){
y.ins += i + 1;
kswx_push_cigar(cigars2, 1, i + 1);
}
if(j >= 0){
y.del += j + 1;
kswx_push_cigar(cigars2, 2, j + 1);
}
} else {
y.qb += i + 1;
y.tb += j + 1;
}
reverse_u32list(cigars2);
y.aln = y.mat + y.mis + y.ins + y.del;
return y;
}
static inline kswx_t kswx_refine_affine_alignment_5q(uint8_t *query, int qb, uint8_t *target, int tb, int W, uint8_t QCLP, uint8_t QMIS, uint8_t QDEL, uint8_t QEXT, uint8_t *qvs[7], u32list *cigars, u8list *mem_cache, u32list *cigars2){
kswx_t y;
uint32_t *rh, *re, SCORE_INF;
int *zb, *ze, *zw;
int ql, tl, rl, _zb, _ze, tx, qx;
int qe, te;
uint8_t *z, *zi;
uint8_t d, qmat[4], qins, qdel[4];
register uint32_t h1, h, m, e, f, t;
long long i, j;
int op, len;
SCORE_INF = 0xFFFFFFFFU >> 1;
clear_u32list(cigars2);
qe = qb; te = tb;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0: qe += len; te += len; break;
case 1: qe += len; break;
default: te += len;
}
}
ql = qe - qb;
tl = te - tb;
if(ql == 0 || tl == 0) return KSWX_NULL;
rl = tl;
clear_and_encap_u8list(mem_cache,
kswx_roundup8x((tl + 2) * sizeof(uint32_t)) * 2 // rh, re
+ kswx_roundup8x((ql + 2) * sizeof(int)) * 3 // zb, ze, zw
+ kswx_roundup8x(((long long)ql) * rl)); // z
rh = (uint32_t*)(mem_cache->buffer);
re = (uint32_t*)(((void*)rh) + kswx_roundup8x((tl + 2) * sizeof(uint32_t)));
zb = (int*)(((void*)re) + kswx_roundup8x((tl + 2) * sizeof(uint32_t)));
ze = (int*)(((void*)zb) + kswx_roundup8x((ql + 2) * sizeof(int)));
zw = (int*)(((void*)ze) + kswx_roundup8x((ql + 2) * sizeof(int)));
z = (uint8_t*)(((void*)zw) + kswx_roundup8x((ql + 2) * sizeof(int)));
// calculate alignment band
// basic band
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
for(j=0;j<len;j++) zw[qx++] = W;
break;
case 1:
for(j=0;j<len;j++) zw[qx++] = W + len;
break;
default:
zw[qx] += len;
}
}
// extending bandwidth around indels
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
qx += len;
break;
case 1:
for(j=1;j<len&&j<qx;j++) zw[qx-j] += len - j;
qx += len - 1;
for(j=1;j<len&&j+qx<ql;j++) zw[qx+j] += len - j;
qx ++;
break;
default:
for(j=1;j<len&&j<qx;j++) zw[qx-j] += len - j;
for(j=1;j<len&&j+qx<ql;j++) zw[qx+j] += len - j;
}
}
// generate band region
tx = qx = 0;
for(i=0;i<(int)cigars->size;i++){
op = cigars->buffer[i] & 0xFU;
len = cigars->buffer[i] >> 4;
switch(op){
case 0:
for(j=0;j<len;j++){
_zb = tx - zw[qx]; if(_zb < 0) _zb = 0;
_ze = tx + 1 + zw[qx]; if(_ze > tl) _ze = tl;
zb[qx] = _zb;
ze[qx] = _ze;
tx ++;
qx ++;
}
break;
case 1:
for(j=0;j<len;j++){
_zb = tx - zw[qx]; if(_zb < 0) _zb = 0;
_ze = tx + 1 + zw[qx]; if(_ze > tl) _ze = tl;
zb[qx] = _zb;
ze[qx] = _ze;
qx ++;
}
break;
default:
tx += len;
}
}
// trim band beg
_zb = 0;
for(i=0;i<ql;i++){
if(zb[i] < _zb) zb[i] = _zb;
else if(zb[i] > _zb) _zb = zb[i];
}
// trim band end
_ze = tl;
for(i=ql-1;i>=0;i--){
if(ze[i] > _ze) ze[i] = _ze;
else if(ze[i] < _ze) _ze = ze[i];
}
// perform alignment
rh[0] = 0;
for(i=1;i<=tl;i++) rh[i] = rh[i - 1] + QCLP;
for(i=0;i<=tl;i++) re[i] = SCORE_INF;
for(i=0;i<ql;i++){
if(zb[i] == 0){
h1 = i * QCLP;
f = h1 + QCLP;
} else {
h1 = f = SCORE_INF;
}
zi = z + (i * rl);
for(j=0;j<4;j++){
if(j == query[i + qb]) qmat[j] = 0;
else if(j == qvs[5][i + qb]) qmat[j] = qvs[1][i + qb];