/usr/include/blasr/algorithms/alignment/AffineKBandAlign.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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#define _BLASR_AFFINE_KBAND_ALIGN_HPP_
#include <cassert>
#include <vector>
#include <iostream>
#include "NucConversion.hpp"
#include "defs.h"
#include "matrix/FlatMatrix.hpp"
#include "datastructures/alignment/Alignment.hpp"
#include "KBandAlign.hpp"
template<typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment>
int AffineKBandAlign(T_QuerySequence &pqSeq, T_TargetSequence &ptSeq,
int matchMat[5][5],
int hpInsOpen, int hpInsExtend, int insOpen, int insExtend,
int del, int k,
vector<int> &scoreMat,
vector<Arrow> & pathMat,
vector<int> &hpInsScoreMat,
vector<Arrow> &hpInsPathMat,
vector<int> &insScoreMat,
vector<Arrow> &insPathMat,
T_Alignment &alignment,
AlignmentType alignType) {
//
// Make a copy of the sequences that is guaranteed to be in 3-bit format
// for quick access to the score array.
//
int INF_SCORE = INF_INT - 1000;
T_QuerySequence qSeq;
T_TargetSequence tSeq;
// CreateThreeBitSequence(pqSeq, qSeq);
// CreateThreeBitSequence(ptSeq, tSeq);
qSeq.seq = pqSeq.seq;
qSeq.length= pqSeq.length;
tSeq.seq = ptSeq.seq;
tSeq.length = ptSeq.length;
DNALength tLen, qLen;
SetKBoundedLengths(tSeq.length, qSeq.length, k, tLen, qLen);
//
//
// Allow for length up to diagonal + k + 1 for boundary.
//
// Allow for width:
// diagonal (1)
// up to k insertions (k)
// up to k deletions (k)
// boundary on left side of matrix (1)
//
// if (qLen + k > tLen and qLen < tLen) {
// k = tLen - qLen +1;
// }
DNALength nCols = 2*k + 1;
VectorIndex totalMatSize = (qLen + 1) * nCols;
//
// For now the scoreMat and path mat maintained outside this
// function so that they may have different sizes from the affine
// matrices.
//
if (scoreMat.size() < totalMatSize) {
scoreMat.resize(totalMatSize);
pathMat.resize(totalMatSize);
}
if (hpInsScoreMat.size() < totalMatSize) {
hpInsScoreMat.resize(totalMatSize);
hpInsPathMat.resize(totalMatSize);
insScoreMat.resize(totalMatSize);
insPathMat.resize(totalMatSize);
}
//
// Initialze matrices
//
std::fill(scoreMat.begin(), scoreMat.begin() + totalMatSize, 0);
std::fill(pathMat.begin(), pathMat.begin() + totalMatSize, NoArrow);
std::fill(hpInsScoreMat.begin(), hpInsScoreMat.begin() + totalMatSize, 0);
std::fill(hpInsPathMat.begin(), hpInsPathMat.begin() + totalMatSize, NoArrow);
std::fill(insScoreMat.begin(), insScoreMat.begin() + totalMatSize, 0);
std::fill(insPathMat.begin(), insPathMat.begin() + totalMatSize, NoArrow);
//
// Initialize the boundaries of the DP matrix.
//
int q, t;
if (alignType != TargetFit) {
insScoreMat[rc2index(0, k, nCols)] = 0;
insPathMat[rc2index(0, k, nCols)] = AffineInsOpen;
for (q = 1; q <=k && q < (int) qLen + 1; q++ ){
insScoreMat[rc2index(q, k - q, nCols)] = q * insExtend + insOpen;
insPathMat[rc2index(q, k-q, nCols)] = AffineInsUp;
}
}
else if (alignType == TargetFit) {
//
// Allow free gap penalties at the beginning of the alignment.
//
insScoreMat[rc2index(0, k, nCols)] = 0;
insPathMat[rc2index(0, k, nCols)] = AffineInsOpen;
for (q = 1; q <= k && q < (int) qLen + 1; q++ ){
insScoreMat[rc2index(q, k - q, nCols)] = 0;
insPathMat[rc2index(q, k-q, nCols)] = AffineInsUp;
}
}
//
// Assign score for (0,0) position in matrix -- aligning a gap to a gap
// which should just be a finished alignment. There is no cost for
// gap-gap alignment.
//
hpInsScoreMat[rc2index(0,k,nCols)] = 0;
hpInsPathMat[rc2index(0,k,nCols)] = AffineHPInsOpen;
for (q = 1; q <= k && q < (int) qLen + 1; q++) {
hpInsScoreMat[rc2index(q, k - q, nCols)] = q * hpInsExtend + hpInsOpen;
hpInsPathMat[rc2index(q,k-q,nCols)] = AffineHPInsUp;
}
for (t = k+1; t < (int) nCols; t++ ) {
hpInsScoreMat[rc2index(0, t, nCols)] = INF_SCORE;// hpInsOpen + (t - k) * hpInsExtend;//; //INF_SCORE;
hpInsPathMat[t] = NoArrow; //AffineHPInsOpen ; //NoArrow;
insScoreMat[t] = INF_SCORE; //insOpen + (t - k) * insExtend; //INF_SCORE;
insPathMat[t] = NoArrow; //AffineInsOpen; //NoArrow;
}
for (q = 1; q <= k && q < (int) qLen + 1; q++) {
scoreMat[rc2index(q, k - q, nCols)] = insScoreMat[rc2index(q,k-q,nCols)];
pathMat[rc2index(q, k - q , nCols)] = AffineInsClose;
}
for (t = 1; t <= (int) k; t++) {
scoreMat[rc2index(0, t + k , nCols)] = t * del;
pathMat[rc2index(0, t + k , nCols)] = Left;
}
//
// The recurrence relation here is a slight modification of the
// standard affine gap alignment. Deletions are non-affine. Insertions
// are affine with different scores for homopolymer insertions, and
// an affine score for mixed insertions.
//
int matchScore, delScore;
int hpInsExtendScore, hpInsOpenScore, insOpenScore, insExtendScore;
int minHpInsScore, minInsScore;
for (q = 1; q <= (int) qLen; q++) {
for (t = q - k; t < (int) q + k + 1; t++) {
if (t < 1) {
continue;
}
if ((DNALength) t > tLen) {
break;
}
VectorIndex upper = rc2index(q-1, k + t - q + 1, nCols);
VectorIndex curIndex = rc2index(q, k + t - q, nCols);
if (t < q + k)
hpInsOpenScore = scoreMat[upper] + hpInsOpen;
else
hpInsOpenScore = INF_SCORE;
//
// The homopolymer insertion score is defined only when the previous nucleotide
// is the same as the current, in which case the homopolymer insertion score
// is used. If the current and previous nucleotide in the query are different,
// the extension is not possible, and the best that can happen is a gap open.
//
if (q > 1 and qSeq[q-1] == qSeq[q-2]) {
if (t < q + k)
hpInsExtendScore = hpInsScoreMat[upper] + hpInsExtend;
else
hpInsExtendScore = INF_SCORE;
}
else {
hpInsExtendScore = INF_SCORE;
}
//
// Since this is only allowing insertions, this grid has only horizontal and
// elevation arrows.
//
if (hpInsOpenScore < hpInsExtendScore) {
hpInsPathMat[curIndex] = AffineHPInsOpen;
minHpInsScore = hpInsOpenScore;
}
else {
hpInsPathMat[curIndex] = AffineHPInsUp;
minHpInsScore = hpInsExtendScore;
}
hpInsScoreMat[curIndex] = minHpInsScore;
if (t < q + k) {
insOpenScore = scoreMat[upper] + insOpen;
insExtendScore = insScoreMat[upper] + insExtend;
}
else {
insOpenScore = INF_SCORE;
insExtendScore = INF_SCORE;
}
if (insOpenScore < insExtendScore) {
insPathMat[curIndex] = AffineInsOpen;
minInsScore = insOpenScore;
}
else {
insPathMat[curIndex] = AffineInsUp;
minInsScore = insExtendScore;
}
insScoreMat[curIndex] = minInsScore;
// On left boundary of k-band.
// do not allow deletions of t.
if (t == q - k) {
delScore = INF_SCORE;
}
else {
// cur row = q
// cur col = t - q
// prev col therefore t - q - 1
// and offset from diagonal is k + t - q - 1
delScore = scoreMat[rc2index(q, k + t - q - 1, nCols)] + del;
}
// cur row = q
// cur col = t - q
// cur query index = q - 1
// cur target index = t - 1
// therefore match row (up) = q
// match col (left, but since up shifted right) = t - q
assert(rc2index(q - 1, k + t - q, nCols) < scoreMat.size());
assert(t-1 >= 0);
assert(q-1 >= 0);
matchScore = scoreMat[rc2index(q - 1, k + t - q, nCols)] + matchMat[ThreeBit[qSeq.seq[q-1]]][ThreeBit[tSeq.seq[t-1]]];
//
// Possibly on right boundary of k-band, in which
// case do not allow insertions from q.
int minScore = MIN(matchScore, MIN(delScore, MIN(minInsScore, minHpInsScore)));
curIndex = rc2index(q, k + t - q, nCols);
assert(curIndex < scoreMat.size());
scoreMat[curIndex] = minScore;
if (minScore == matchScore) {
pathMat[curIndex] = Diagonal;
}
else if (minScore == delScore) {
pathMat[curIndex] = Left;
}
else if (minScore == minInsScore) {
pathMat[curIndex] = AffineInsClose;
}
else {
pathMat[curIndex] = AffineHPInsClose;
}
}
}
/*
std::cout << "tracing back from: " << q << ", " << t << std::endl;
std::cout << "match score: " << std::endl;
PrintFlatMatrix(&scoreMat[0], qLen + 1, nCols, std::cout);
std::cout << " path: " << std::endl;
PrintFlatMatrix(pathMat, qLen + 1, nCols, std::cout);
std::cout << "hp score: " << std::endl;
PrintFlatMatrix(&hpInsScoreMat[0], qLen + 1, nCols, std::cout);
std::cout << "hp path: " << std::endl;
PrintFlatMatrix(hpInsPathMat, qLen + 1, nCols, std::cout);
std::cout << "normal affine ins score: " << std::endl;
PrintFlatMatrix(&insScoreMat[0], qLen + 1, nCols, std::cout);
std::cout << "normal affine ins path: " << std::endl;
PrintFlatMatrix(&insPathMat[0], qLen + 1, nCols, std::cout);
*/
vector<Arrow> optAlignment;
// First find the end position matrix.
int minScoreTPos, minScore;
int minScoreQPos;
if (alignType == Global) {
q = qLen ;
t = k - ((int)qLen - (int)tLen);
}
else if (alignType == QueryFit) {
q = qLen;
minScoreTPos = max(q-k,1);
DNALength index = rc2index(qLen, k + minScoreTPos - q, nCols);
minScore = scoreMat[index];
for (t = q - k; t < (int) q + k + 1; t++) {
if (t < 1) { continue;}
if (t > tLen) { break;}
int index = rc2index(qLen,k + t - q,nCols);
if (scoreMat[index] < minScore) {
minScoreTPos = t;
minScore = scoreMat[index ];
}
}
t = k - ((int)qLen - minScoreTPos);
}
else if (alignType == TargetFit) {
t = tLen;
int qStart = max(0,min((int)qLen, (int)tLen) - max(0, k - max(((int)tLen) - ((int)qLen), 0)));
int qEnd = min(qLen, tLen + k) + 1;
minScoreQPos = qStart;
int index = rc2index(minScoreQPos, k - (minScoreQPos - tLen), nCols);
minScore = scoreMat[index];
for (q = qStart; q < qEnd; q++) {
// add to k since this is going up.
index = rc2index(q, k + (q - tLen), nCols);
if (scoreMat[index] < minScore) {
minScoreQPos = q;
minScore = scoreMat[index];
}
}
q = minScoreQPos;
t = (k+((int)q-(int)tLen));
}
int optScore = scoreMat[rc2index(q, t, nCols)];
Arrow arrow;
MatrixLabel curMatrix = Match;
while ((q > 0) or
(q == 0 and t > k)) {
assert(t < 2*k+1);
if (curMatrix == Match) {
arrow = pathMat[rc2index(q,t, nCols)];
if (arrow == Diagonal) {
optAlignment.push_back(arrow);
q--;
}
else if (arrow == Left) {
optAlignment.push_back(arrow);
t--;
}
//
// The following two conditions change matrices
// without changing coordinates, since the gap close
// just changes state without adding to the alignment.
//
else if (arrow == AffineInsClose) {
curMatrix = AffineIns;
}
else if (arrow == AffineHPInsClose) {
curMatrix = AffineHPIns;
}
}
else if (curMatrix == AffineHPIns) {
//
// The current
arrow = hpInsPathMat[rc2index(q,t,nCols)];
if (arrow == AffineHPInsOpen) {
curMatrix = Match;
}
else if (arrow != AffineHPInsUp) {
std::cout << "ERROR! Affine homopolymer insertion path matrix MUST only have UP or OPEN arrows." << std::endl;
assert(0);
}
optAlignment.push_back(Up);
q--;
t++;
}
else if (curMatrix == AffineIns) {
arrow = insPathMat[rc2index(q,t,nCols)];
if (arrow == AffineInsOpen) {
curMatrix = Match;
}
else if (arrow != AffineInsUp) {
std::cout << "ERROR! Affine insertion path matrix MUST only have UP or OPEN arrows."<<std::endl;
assert(0);
}
optAlignment.push_back(Up);
q--;
t++;
}
else {
std::cout << "ERROR in affine local alignment, matrix is: " << curMatrix << std::endl;
assert(0);
}
}
// qSeq.Free();
// tSeq.Free();
std::reverse(optAlignment.begin(), optAlignment.end());
alignment.ArrowPathToAlignment(optAlignment);
return optScore;
}
#endif // _BLASR_AFFINE_KBAND_ALIGN_HPP_
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