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nw2p.c
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/* Philip T.L.C. Clausen Jan 2017 [email protected] */
/*
* Copyright (c) 2017, Philip Clausen, Technical University of Denmark
* All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#include <stdlib.h>
#include <string.h>
#include "nw.h"
#include "penalties.h"
#include "pherror.h"
#include "stdnuc.h"
AlnScore NW2P(const long unsigned *template, const unsigned char *queryOrg, int k, int t_s, int t_e, int q_s, int q_e, Aln *aligned, NWmat *matrices, int template_length) {
int m, n, t_len, q_len, thisScore, nuc_pos, W1, U, W2, U2, MM;
int pos[2], *tmp, **d, *D_ptr, *D_prev, Q, Q_prev, *P_ptr, *P_prev;
int Q2, Q2_prev, *P2_ptr, *P2_prev;
unsigned char *query, t_nuc, *E, *E_ptr, e;
AlnScore Stat;
Penalties *rewards;
rewards = matrices->rewards;
W1 = rewards->W1;
U = rewards->U;
W2 = rewards->W2;
U2 = rewards->U2;
MM = rewards->MM;
d = rewards->d;
q_len = q_e - q_s;
t_len = t_e - t_s;
aligned->start = 0;
aligned->end = 0;
if(t_len < 0) {
t_len += template_length;
}
query = (unsigned char*)(queryOrg + q_s);
Stat.pos = 0;
if(t_len == 0 || q_len == 0) {
if(t_len == q_len) {
Stat.len = 0;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = 0;
Stat.score = 0;
aligned->s[0] = 0;
} else if(t_len == 0) {
Stat.len = q_len;
Stat.match = 0;
Stat.tGaps = q_len;
Stat.qGaps = 0;
Stat.score = W1 + (q_len - 1) * U;
if((W2 + (q_len - 1) * U2) < Stat.score) {
Stat.score = (W2 + (q_len - 1) * U2);
}
memset(aligned->s, '_', q_len);
aligned->s[q_len] = 0;
memset(aligned->t, 5, q_len);
memcpy(aligned->q, query, q_len);
} else {
Stat.len = t_len;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = t_len;
Stat.score = W1 + (t_len - 1) * U;
if((W2 + (t_len - 1) * U2) < Stat.score) {
Stat.score = (W2 + (t_len - 1) * U2);
}
memset(aligned->s, '_', t_len);
aligned->s[t_len] = 0;
memset(aligned->q, 5, t_len);
m = t_len;
nuc_pos = (t_e ? t_e : aligned->pos) - 1;
while(m--) {
aligned->t[m] = getNuc(template, nuc_pos);
if(--nuc_pos < 0) {
nuc_pos = aligned->pos - 1;
}
}
}
return Stat;
}
/* check matrix size */
if(matrices->NW_q <= q_len) {
matrices->NW_q = q_len << 1;
free(matrices->D[0]);
free(matrices->P[0]);
free(matrices->P2[0]);
matrices->D[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->P[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->P2[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->D[1] = matrices->D[0] + matrices->NW_q;
matrices->P[1] = matrices->P[0] + matrices->NW_q;
matrices->P2[1] = matrices->P[0] + matrices->NW_q;
}
if(matrices->NW_s <= ((q_len + 1) * (t_len + 1))) {
matrices->NW_s = ((q_len + 2) * (t_len + 2));
free(matrices->E);
matrices->E = smalloc(matrices->NW_s);
}
/* fill in start penalties */
D_ptr = matrices->D[0];
D_prev = matrices->D[1];
P_ptr = matrices->P[0];
P_prev = matrices->P[1];
P2_ptr = matrices->P2[0];
P2_prev = matrices->P2[1];
E = matrices->E;
thisScore = (t_len + q_len) * (MM + U + W1);
Stat.score = thisScore;
if(0 < k) {
E_ptr = E;
for(m = 0; m < t_len; ++m) {
E_ptr[q_len] = 0;
E_ptr += (q_len + 1);
}
if(k == 1) {
for(n = q_len - 1; n >= 0; --n) {
Q = W1 + (q_len - 1 - n) * U;
Q2 = W2 + (q_len - 1 - n) * U2;
if(Q2 < Q) {
D_prev[n] = W1 + (q_len - 1 - n) * U;
E_ptr[n] = 2;
} else {
D_prev[n] = W2 + (q_len - 1 - n) * U2;
E_ptr[n] = 4;
}
P_prev[n] = thisScore;
P2_prev[n] = thisScore;
}
E_ptr[q_len - 1] = 86;
E_ptr[q_len] = 0;
D_prev[q_len] = 0;
P_prev[q_len] = 0;
P2_prev[q_len] = 0;
} else {
for(n = q_len; n >= 0; --n) {
D_prev[n] = 0;
P_prev[n] = thisScore;
P2_prev[n] = thisScore;
E_ptr[n] = 0;
}
}
} else {
E_ptr = E;
for(m = 0; m < t_len; ++m) {
Q = W1 + (t_len - 1 - m) * U;
Q2 = W2 + (t_len - 1 - m) * U2;
if(Q2 < Q) {
E_ptr[q_len] = 3;
} else {
E_ptr[q_len] = 5;
}
E_ptr += (q_len + 1);
}
E_ptr[-1] = 168;
for(n = q_len - 1; n >= 0; --n) {
Q = W1 + (q_len - 1 - n) * U;
Q2 = W2 + (q_len - 1 - n) * U2;
if(Q2 < Q) {
D_prev[n] = Q;
E_ptr[n] = 2;
} else {
D_prev[n] = Q2;
E_ptr[n] = 4;
}
P_prev[n] = thisScore;
P2_prev[n] = thisScore;
}
E_ptr[q_len - 1] = 86;
E_ptr[q_len] = 0;
D_prev[q_len] = 0;
P_prev[q_len] = 0;
P2_prev[q_len] = 0;
}
E_ptr -= (q_len + 1);
/*
E 0
D 1
Q 2, 16
P 3, 32
Q2 4, 64
P2 5, 128
*/
/* Perform NW */
pos[0] = 0;
for(m = t_len - 1, nuc_pos = t_e - 1; m >= 0; --m, --nuc_pos) {
if(nuc_pos < 0) {
nuc_pos = template_length - 1;
}
D_ptr[q_len] = (0 < k) ? 0 : (W1 + (t_len - 1 - m) * U);
Q_prev = (t_len + q_len) * (MM + U + W1);
Q2_prev = (t_len + q_len) * (MM + U2 + W2);
t_nuc = getNuc(template, nuc_pos);
for(n = q_len - 1; n >= 0; --n) {
E_ptr[n] = 0;
/* update Q and P, gap openings */
Q = D_ptr[n + 1] + W1;
P_ptr[n] = D_prev[n] + W1;
if(Q < P_ptr[n]) {
D_ptr[n] = P_ptr[n];
e = 3;
} else {
D_ptr[n] = Q;
e = 2;
}
/* update Q and P, gap extensions */
/* mark bit 4 and 5 as possible gap-opennings, if necesarry */
thisScore = Q_prev + U;
if(Q < thisScore) {
Q = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 2;
}
} else {
E_ptr[n] |= 16;
}
thisScore = P_prev[n] + U;
if(P_ptr[n] < thisScore) {
P_ptr[n] = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 3;
}
} else {
E_ptr[n] |= 32;
}
/* update Q2 and P2, gap openings */
Q2 = D_ptr[n + 1] + W2;
P2_ptr[n] = D_prev[n] + W2;
if(Q2 < P2_ptr[n]) {
D_ptr[n] = P2_ptr[n];
e = 5;
} else {
D_ptr[n] = Q2;
e = 4;
}
/* update Q2 and P2, gap extensions */
/* mark bit 6 and 7 as possible gap-opennings, if necesarry */
thisScore = Q2_prev + U2;
if(Q2 < thisScore) {
Q2 = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 4;
}
} else {
E_ptr[n] |= 64;
}
thisScore = P2_prev[n] + U2;
if(P2_ptr[n] < thisScore) {
P2_ptr[n] = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 5;
}
} else {
E_ptr[n] |= 128;
}
/* Update D, match */
thisScore = D_prev[n + 1] + d[t_nuc][query[n]];
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
E_ptr[n] |= e;
}
Q_prev = Q;
}
E_ptr -= (q_len + 1);
if(k < 0 && Stat.score < *D_ptr) {
Stat.score = *D_ptr;
pos[0] = m;
}
tmp = D_ptr;
D_ptr = D_prev;
D_prev = tmp;
tmp = P_ptr;
P_ptr = P_prev;
P_prev = tmp;
tmp = P2_ptr;
P2_ptr = P2_prev;
P2_prev = tmp;
}
E_ptr = E;
/* get start position of alignment */
if(k < 0) {
pos[1] = 0;
if(k == -2) {
for(n = 0; n < q_len; ++n) {
if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = (aligned->start = n);
}
}
}
} else {
Stat.score = *D_prev;
pos[0] = 0;
pos[1] = 0;
}
/* make back tracking */
m = pos[0];
n = pos[1];
E_ptr = E + (m * (q_len + 1));
nuc_pos = m + t_s;
Stat.len = 0;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = 0;
while(E_ptr[n] != 0) {
if(nuc_pos == template_length) {
nuc_pos = 0;
}
e = E_ptr[n] & 15;
if(e == 1) {
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = query[n];
aligned->s[Stat.len] = (aligned->t[Stat.len] == aligned->q[Stat.len]) ? '|' : '_';
++Stat.match;
++nuc_pos;
E_ptr += (q_len + 1);
++n;
} else if(e == 2) {
/* Q */
while(!(E_ptr[n] & 16)) {
aligned->t[Stat.len] = 5;
aligned->q[Stat.len] = query[n];
aligned->s[Stat.len] = '_';
++n;
++Stat.len;
++Stat.tGaps;
}
aligned->t[Stat.len] = 5;
aligned->q[Stat.len] = query[n];
aligned->s[Stat.len] = '_';
++n;
++Stat.tGaps;
} else if(e == 3) {
/* P */
while(!(E_ptr[n] & 32)) {
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = 5;
aligned->s[Stat.len] = '_';
++nuc_pos;
E_ptr += (q_len + 1);
++Stat.len;
++Stat.qGaps;
}
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = 5;
aligned->s[Stat.len] = '_';
++nuc_pos;
E_ptr += (q_len + 1);
++Stat.qGaps;
} else if(e == 4) {
/* Q2 */
while(!(E_ptr[n] & 64)) {
aligned->t[Stat.len] = 5;
aligned->q[Stat.len] = query[n];
aligned->s[Stat.len] = '_';
++n;
++Stat.len;
++Stat.tGaps;
}
aligned->t[Stat.len] = 5;
aligned->q[Stat.len] = query[n];
aligned->s[Stat.len] = '_';
++n;
++Stat.tGaps;
} else /*if(e == 5)*/ {
/* P2 */
while(!(E_ptr[n] & 128)) {
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = 5;
aligned->s[Stat.len] = '_';
++nuc_pos;
E_ptr += (q_len + 1);
++Stat.len;
++Stat.qGaps;
}
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = 5;
aligned->s[Stat.len] = '_';
++nuc_pos;
E_ptr += (q_len + 1);
++Stat.qGaps;
}
++Stat.len;
}
aligned->s[Stat.len] = 0;
aligned->end = q_len - n;
return Stat;
}
AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, int k, int t_s, int t_e, int q_s, int q_e, Aln *aligned, int band, NWmat *matrices, int template_length) {
int m, n, t_len, q_len, thisScore, nuc_pos, pos[2];
int bq_len, halfBand, sn, en, sq, eq, q_pos, c_pos, W1, U, MM;
int *D_ptr, *D_prev, Q, Q_prev, *P_ptr, *P_prev, *tmp, **d;
unsigned char *query, t_nuc, *E, *E_ptr, e;
AlnScore Stat;
Penalties *rewards;
rewards = matrices->rewards;
W1 = rewards->W1;
U = rewards->U;
MM = rewards->MM;
d = rewards->d;
q_len = q_e - q_s;
t_len = t_e - t_s;
aligned->start = 0;
aligned->end = 0;
if(t_len < 0) {
t_len += template_length;
}
query = (unsigned char*)(queryOrg + q_s);
Stat.pos = 0;
if(t_len == 0 || q_len == 0) {
if(t_len == q_len) {
Stat.score = 0;
Stat.len = 0;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = 0;
aligned->s[0] = 0;
} else if(t_len == 0) {
Stat.len = q_len;
Stat.match = 0;
Stat.tGaps = q_len;
Stat.qGaps = 0;
Stat.score = W1 + (q_len - 1) * U;
memset(aligned->s, '_', q_len);
aligned->s[q_len] = 0;
memset(aligned->t, 5, q_len);
memcpy(aligned->q, query, q_len);
} else {
Stat.len = t_len;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = t_len;
Stat.score = W1 + (t_len - 1) * U;
memset(aligned->s, '_', t_len);
aligned->s[t_len] = 0;
memset(aligned->q, 5, t_len);
m = t_len;
nuc_pos = (t_e ? t_e : aligned->pos) - 1;
while(m--) {
aligned->t[m] = getNuc(template, nuc_pos);
if(--nuc_pos < 0) {
nuc_pos = aligned->pos - 1;
}
}
}
return Stat;
}
/* ensure that band is equal */
if(band & 1) {
++band;
}
halfBand = band >> 1;
/* check matrix size */
if(matrices->NW_q <= band) {
matrices->NW_q = band << 1;
free(matrices->D[0]);
free(matrices->P[0]);
matrices->D[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->P[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->D[1] = matrices->D[0] + matrices->NW_q;
matrices->P[1] = matrices->P[0] + matrices->NW_q;
}
if(matrices->NW_s <= ((band + 2) * (t_len + 1))) {
matrices->NW_s = ((band + 3) * (t_len + 2));
free(matrices->E);
matrices->E = smalloc(matrices->NW_s);
}
/* fill in start penalties */
bq_len = band + 1; /* (band + 1) ~ q_len */
D_ptr = matrices->D[0];
D_prev = matrices->D[1];
P_ptr = matrices->P[0];
P_prev = matrices->P[1];
E = matrices->E;
thisScore = (t_len + q_len) * (MM + U + W1);
Stat.score = thisScore;
E_ptr = E + (t_len * (bq_len + 1));
c_pos = (t_len + q_len) >> 1;
sn = q_len - 1 - (c_pos - halfBand);
if(k != 2) {
for(n = sn - 1; n >= 0; --n) {
D_prev[n] = W1 + (sn - n - 1) * U;
P_prev[n] = thisScore;
E_ptr[n] = 3;
}
E_ptr[sn - 1] = 18;
E_ptr[sn] = 0;
D_prev[sn] = 0;
P_prev[sn] = 0;
} else {
for(n = sn; n >= 0; --n) {
D_prev[n] = 0;
P_prev[n] = thisScore;
E_ptr[n] = 0;
}
}
E_ptr -= (bq_len + 1);
/* Perform banded NW */
pos[0] = 0;
pos[1] = 0;
en = 0;
c_pos = (t_len + q_len) >> 1;
for(m = t_len - 1, nuc_pos = t_e - 1; m >= 0; --m, --nuc_pos, --c_pos) {
if(nuc_pos < 0) {
nuc_pos = template_length - 1;
}
/* get banded boundaries, w.r.t. query */
sq = c_pos + halfBand;
eq = c_pos - halfBand;
if(eq < 0) {
eq = 0;
++en;
} else {
en = 0;
}
/* get start penalties */
Q_prev = (t_len + q_len) * (MM + U + W1);
/* check boundaries */
if(sq < (q_len - 1)) {
sn = bq_len - 1;
D_ptr[bq_len] = (t_len + q_len) * (MM + U + W1);
E_ptr[bq_len] = 37;
} else {
sq = q_len - 1;
sn = en + (q_len - eq);
D_ptr[sn] = (0 < k) ? 0 : (W1 + (t_len - 1 - m) * U);
E_ptr[sn] = (0 < k) ? 0 : 37;
--sn;
}
t_nuc = getNuc(template, nuc_pos);
for(n = sn, q_pos = sq; n > en; --q_pos, --n) {
E_ptr[n] = 0;
/* update Q and P, gap openings */
Q = D_ptr[n + 1] + W1;
P_ptr[n] = D_prev[n - 1] + W1;
if(Q < P_ptr[n]) {
D_ptr[n] = P_ptr[n];
e = 4;
} else {
D_ptr[n] = Q;
e = 2;
}
/* update Q and P, gap extensions */
/* mark bit 4 and 5 as possible gap-opennings, if necesarry */
thisScore = Q_prev + U;
if(Q < thisScore) {
Q = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 3;
}
} else {
E_ptr[n] |= 16;
}
thisScore = P_prev[n - 1] + U;
if(P_ptr[n] < thisScore) {
P_ptr[n] = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 5;
}
} else {
E_ptr[n] |= 32;
}
/* Update D, match */
thisScore = D_prev[n] + d[t_nuc][query[q_pos]];
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
E_ptr[n] |= e;
}
Q_prev = Q;
}
/* handle banded boundary */
E_ptr[n] = 0;
/* update Q gap */
Q = D_ptr[n + 1] + W1;
thisScore = Q_prev + U;
if(Q < thisScore) {
Q = thisScore;
e = 3;
} else {
e = 2;
E_ptr[n] |= 16;
}
/* update unavailable P gap */
P_ptr[n] = (t_len + q_len) * (MM + U + W1);
/* Update D */
D_ptr[n] = D_prev[n] + d[t_nuc][query[q_pos]];
/* set D to max, and set E */
if(Q <= D_ptr[n]) {
E_ptr[n] |= 1;
} else {
D_ptr[n] = Q;
E_ptr[n] |= e;
}
/* continue as usual */
E_ptr -= (bq_len + 1);
if(eq == 0 && k < 0 && Stat.score < D_ptr[n]) {
Stat.score = D_ptr[n];
pos[0] = m;
pos[1] = n;
}
tmp = D_ptr;
D_ptr = D_prev;
D_prev = tmp;
tmp = P_ptr;
P_ptr = P_prev;
P_prev = tmp;
}
E_ptr = E;
/* get start position of alignment */
q_pos = 0;
if(pos[0] == 0) {
pos[1] = en;
Stat.score = D_prev[en];
}
if(k == -2) {
for(n = en; n < bq_len; ++n) {
if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = n;
q_pos = n - en;
}
}
}
aligned->start = q_pos;
/* back tracking */
m = pos[0];
n = pos[1];
E_ptr = E + (m * (bq_len + 1));
nuc_pos = m + t_s;
Stat.len = 0;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = 0;
while(E_ptr[n] != 0) {
if(nuc_pos == template_length) {
nuc_pos = 0;
}
if((E_ptr[n] & 7) == 1) {
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = query[q_pos];
aligned->s[Stat.len] = (aligned->t[Stat.len] == aligned->q[Stat.len]) ? '|' : '_';
++Stat.match;
++nuc_pos;
E_ptr += (bq_len + 1);
++q_pos;
} else if((E_ptr[n] & 7) >= 4) {
while(!(E_ptr[n] >> 4)) {
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = 5;
aligned->s[Stat.len] = '_';
++nuc_pos;
E_ptr += (bq_len + 1);
--n;
++Stat.len;
++Stat.qGaps;
}
aligned->t[Stat.len] = getNuc(template, nuc_pos);
aligned->q[Stat.len] = 5;
aligned->s[Stat.len] = '_';
++nuc_pos;
E_ptr += (bq_len + 1);
--n;
++Stat.qGaps;
} else {
while(!(E_ptr[n] >> 3)) {
aligned->t[Stat.len] = 5;
aligned->q[Stat.len] = query[q_pos];
aligned->s[Stat.len] = '_';
++n;
++q_pos;
++Stat.len;
++Stat.tGaps;
}
aligned->t[Stat.len] = 5;
aligned->q[Stat.len] = query[q_pos];
aligned->s[Stat.len] = '_';
++n;
++q_pos;
++Stat.tGaps;
}
++Stat.len;
}
aligned->s[Stat.len] = 0;
aligned->end = q_len - q_pos;
return Stat;
}
AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg, int k, int t_s, int t_e, int q_s, int q_e, NWmat *matrices, int template_length) {
int m, n, t_len, q_len, thisScore, nuc_pos, W1, U, MM, pos[2];
int *D_ptr, *D_prev, Q, Q_prev, *P_ptr, *P_prev, *tmp, **d;
unsigned char *query, t_nuc, *E, *E_ptr, e;
AlnScore Stat;
Penalties *rewards;
rewards = matrices->rewards;
W1 = rewards->W1;
U = rewards->U;
MM = rewards->MM;
d = rewards->d;
t_len = t_e - t_s;
q_len = q_e - q_s;
if(t_len < 0) {
t_len += template_length;
}
query = (unsigned char*)(queryOrg + q_s);
Stat.pos = 0;
if(t_len == 0 || q_len == 0) {
if(t_len == q_len) {
Stat.len = 0;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = 0;
Stat.score = 0;
} else if(t_len == 0) {
Stat.len = q_len;
Stat.match = 0;
Stat.tGaps = q_len;
Stat.qGaps = 0;
Stat.score = W1 + (q_len - 1) * U;
} else {
Stat.len = t_len;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = t_len;
Stat.score = W1 + (t_len - 1) * U;
}
return Stat;
}
/* check matrix size */
if(matrices->NW_q <= q_len) {
matrices->NW_q = q_len << 1;
free(matrices->D[0]);
free(matrices->P[0]);
matrices->D[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->P[0] = smalloc((matrices->NW_q << 1) * sizeof(int));
matrices->D[1] = matrices->D[0] + matrices->NW_q;
matrices->P[1] = matrices->P[0] + matrices->NW_q;
}
if(matrices->NW_s <= ((q_len + 1) * (t_len + 1))) {
matrices->NW_s = ((q_len + 2) * (t_len + 2));
free(matrices->E);
matrices->E = smalloc(matrices->NW_s);
}
/* fill in start penalties */
D_ptr = matrices->D[0];
D_prev = matrices->D[1];
P_ptr = matrices->P[0];
P_prev = matrices->P[1];
E = matrices->E;
thisScore = (t_len + q_len) * (MM + U + W1);
Stat.score = thisScore;
if(0 < k) {
E_ptr = E;
for(m = 0; m < t_len; ++m) {
E_ptr[q_len] = 0;
E_ptr += (q_len + 1);
}
if(k == 1) {
for(n = q_len - 1; n >= 0; --n) {
D_prev[n] = W1 + (q_len - 1 - n) * U;
P_prev[n] = thisScore;
E_ptr[n] = 3;
}
E_ptr[q_len - 1] = 18;
E_ptr[q_len] = 0;
D_prev[q_len] = 0;
P_prev[q_len] = 0;
} else {
for(n = q_len; n >= 0; --n) {
D_prev[n] = 0;
P_prev[n] = thisScore;
E_ptr[n] = 0;
}
}
} else {
E_ptr = E;
for(m = 0; m < t_len; ++m) {
E_ptr[q_len] = 5;
E_ptr += (q_len + 1);
}
E_ptr[-1] = 36;
for(n = q_len - 1; n >= 0; --n) {
D_prev[n] = W1 + (q_len - 1 - n) * U;
P_prev[n] = thisScore;
E_ptr[n] = 3;
}
E_ptr[q_len - 1] = 18;
E_ptr[q_len] = 0;
D_prev[q_len] = 0;
P_prev[q_len] = 0;
}
E_ptr -= (q_len + 1);
/* Perform NW */
pos[0] = 0;
for(m = t_len - 1, nuc_pos = t_e - 1; m >= 0; --m, --nuc_pos) {
if(nuc_pos < 0) {
nuc_pos = template_length - 1;
}
D_ptr[q_len] = (0 < k) ? 0 : (W1 + (t_len - 1 - m) * U);
Q_prev = (t_len + q_len) * (MM + U + W1);
t_nuc = getNuc(template, nuc_pos);
for(n = q_len - 1; n >= 0; --n) {
E_ptr[n] = 0;
/* update Q and P, gap openings */
Q = D_ptr[n + 1] + W1;
P_ptr[n] = D_prev[n] + W1;
if(Q < P_ptr[n]) {
D_ptr[n] = P_ptr[n];
e = 4;
} else {
D_ptr[n] = Q;
e = 2;
}
/* update Q and P, gap extensions */
/* mark bit 4 and 5 as possible gap-opennings, if necesarry */
thisScore = Q_prev + U;
if(Q < thisScore) {
Q = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 3;
}
} else {
E_ptr[n] |= 16;
}
thisScore = P_prev[n] + U;
if(P_ptr[n] < thisScore) {
P_ptr[n] = thisScore;
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
e = 5;
}
} else {
E_ptr[n] |= 32;
}
/* Update D, match */
thisScore = D_prev[n + 1] + d[t_nuc][query[n]];
if(D_ptr[n] <= thisScore) {
D_ptr[n] = thisScore;
E_ptr[n] |= 1;
} else {
E_ptr[n] |= e;
}
Q_prev = Q;
}
E_ptr -= (q_len + 1);
if(k < 0 && Stat.score < *D_ptr) {
Stat.score = *D_ptr;
pos[0] = m;
}
tmp = D_ptr;
D_ptr = D_prev;
D_prev = tmp;
tmp = P_ptr;
P_ptr = P_prev;
P_prev = tmp;
}
E_ptr = E;
/* get start position of alignment */
if(k < 0) {
pos[1] = 0;
if(k == -2) {
for(n = 0; n < q_len; ++n) {
if(Stat.score <= D_prev[n]) {
Stat.score = D_prev[n];
pos[0] = 0;
pos[1] = n;
}
}
}
} else {
Stat.score = *D_prev;
pos[0] = 0;
pos[1] = 0;
}
/* make back tracking */
m = pos[0];
E_ptr = E + (m * (q_len + 1));
n = pos[1];
nuc_pos = m + t_s;
Stat.len = 0;
Stat.match = 0;
Stat.tGaps = 0;
Stat.qGaps = 0;
while(E_ptr[n] != 0) {
if(nuc_pos == template_length) {
nuc_pos = 0;
}
if((E_ptr[n] & 7) == 1) {
++Stat.match;
++nuc_pos;
E_ptr += (q_len + 1);
++n;
} else if((E_ptr[n] & 7) >= 4) {
while(!(E_ptr[n] >> 4)) {
++nuc_pos;
E_ptr += (q_len + 1);
++Stat.len;
++Stat.qGaps;
}
++Stat.qGaps;
++nuc_pos;
E_ptr += (q_len + 1);
} else {