/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp is in libblasr-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define _BLASR_ALIGNMENT_UTILS_IMPL_HPP_
#include <cassert>
using namespace blasr;
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
int ComputeAlignmentScore(Alignment &alignment,
T_QuerySequence &query,
T_TargetSequence &text,
T_ScoreFn &scoreFn,
bool useAffinePenalty) {
VectorIndex b, q, t, l, gi;
int alignmentScore = 0;
for (b = 0; b < alignment.blocks.size(); b++ ) {
for ((q = alignment.qPos + alignment.blocks[b].qPos,
t = alignment.tPos + alignment.blocks[b].tPos,
l = 0) ;
l < alignment.blocks[b].length; q++, t++, l++) {
alignmentScore += scoreFn.Match(text, t, query, q);
}
if (alignment.gaps.size() == alignment.blocks.size() + 1) {
for (gi = 0; gi < alignment.gaps[b+1].size(); gi++) {
if (alignment.gaps[b+1][gi].seq == Gap::Target) {
if (useAffinePenalty) {
alignmentScore += scoreFn.affineOpen + alignment.gaps[b+1][gi].length * scoreFn.affineExtend;
}
else {
alignmentScore += alignment.gaps[b+1][gi].length * scoreFn.ins;
}
}
else {
if (useAffinePenalty) {
alignmentScore += scoreFn.affineOpen + alignment.gaps[b+1][gi].length * scoreFn.affineExtend;
}
else {
alignmentScore += alignment.gaps[b+1][gi].length * scoreFn.del;
}
}
}
}
}
return alignmentScore;
}
template<typename T_QuerySequence, typename T_TargetSequence>
int ComputeAlignmentScore(blasr::Alignment &alignment,
T_QuerySequence &query,
T_TargetSequence &text,
int matchScores[5][5],
int ins,
int del) {
DistanceMatrixScoreFunction<DNASequence, DNASequence> scoreFn(matchScores, ins, del);
return ComputeAlignmentScore(alignment, query, text, scoreFn);
}
template<typename T_ScoreFn>
int ComputeAlignmentScore(std::string &queryStr, std::string &textStr, T_ScoreFn &scoreFn,
bool useAffineScore) {
if (queryStr.size() != textStr.size()) {
std::cout << "Computing alignment score using invalid alignment string." << std::endl;
std::cout << "Bailing out."<< std::endl;
exit(1);
}
VectorIndex i;
int score = 0;
VectorIndex alignStrLen = queryStr.size();
for(i = 0; i < alignStrLen; i++) {
if (queryStr[i] != '-' and
textStr[i] != '-') {
score += scoreFn.scoreMatrix[ThreeBit[(int)queryStr[i]]][ThreeBit[(int)textStr[i]]];
}
else {
if (useAffineScore) {
//
// Compute affine gap scoring. For now this uses symmetric insertion/deletion penalties.
//
unsigned gapEnd = i;
while (gapEnd < queryStr.size() and gapEnd < textStr.size() and
(queryStr[gapEnd] == '-' or textStr[gapEnd] == '-')) {
++gapEnd;
}
int gapLength = gapEnd - i;
score += scoreFn.affineOpen + gapLength * scoreFn.affineExtend;
//
// Advance past gap -1, so that at the top of the for loop i
// will be at the end of the gap.
//
i = gapEnd - 1;
}
else {
//
// Use non-affine gap scoring.
//
if (queryStr[i] == '-' and textStr[i] != '-') {
score += scoreFn.del;
}
else if (queryStr[i] != '-' and textStr[i] == '-') {
score += scoreFn.ins;
}
else {
score += scoreFn.scoreMatrix[4][4];
}
}
}
}
return score;
}
/*
* This should be changed to read any type of alignment, since templates are being
* used.
*/
inline void ReadCompSeqAlignments(std::string &compSeqAlignmentFileName, std::vector<CompSeqAlignment> &alignments) {
std::ifstream in;
CrucialOpen(compSeqAlignmentFileName, in);
CompSeqAlignment alignment;
while (ReadCompSeqAlignment(in, alignment)) {
alignments.push_back(alignment);
}
}
inline void PrintAlignmentStats(Alignment &alignment, std::ostream &out) {
out << " nMatch: " << alignment.nMatch << std::endl;
out << " nMisMatch: " << alignment.nMismatch << std::endl;
out << " nIns: " << alignment.nIns << std::endl;
out << " nDel: " << alignment.nDel << std::endl;
out << " %sim: " << alignment.pctSimilarity << std::endl;
out << " Score: " << alignment.score << std::endl;
}
template<typename T_Alignment>
inline void PrintCompareSequencesAlignmentStats(T_Alignment &alignment, std::ostream &out) {
int lastBlock;
lastBlock = alignment.blocks.size() -1;
int qLength, tLength;
if (lastBlock >= 0) {
qLength = (alignment.blocks[lastBlock].qPos
+ alignment.blocks[lastBlock].length) ;
tLength = (alignment.blocks[lastBlock].tPos
+ alignment.blocks[lastBlock].length);
}
else {
qLength = tLength = 0;
}
//
// First print the query
//
int alignmentQStart;
if (lastBlock >= 0) {
alignmentQStart = alignment.qPos + alignment.qAlignedSeqPos;
}
else {
alignmentQStart = alignment.qAlignedSeqPos;
}
out << alignment.qName
<< " " << alignment.qLength
<< " " << alignmentQStart
<< " " << alignmentQStart + qLength;
if (alignment.qStrand == 0) {
out << " + ";
}
else {
out << " - ";
}
int alignmentTStart;
if (lastBlock >= 0) {
alignmentTStart = alignment.tPos + alignment.tAlignedSeqPos;
}
else {
alignmentTStart = 0;
}
out << " " << alignment.tName
<< " " << alignment.tLength;
if (alignment.tStrand == 0) {
out << " " << alignmentTStart
<< " " << alignmentTStart + tLength;
out << " + ";
}
else {
out << " " << alignment.tLength - (alignmentTStart + tLength)
<< " " << alignment.tLength - (alignmentTStart);
out << " - ";
}
out << alignment.score
<< " " << alignment.nMatch
<< " " << alignment.nMismatch
<< " " << alignment.nIns
<< " " << alignment.nDel
<< " " << (int) alignment.mapQV
<< " ";
}
template<typename T_Alignment>
inline int ReadCompareSequencesAlignmentStats(std::istream &in, T_Alignment &alignment) {
int qEnd, tEnd;
int qLength, tLength;
char qStrand, tStrand;
if (!(in >> alignment.qName )) return 0;
if (!(in >> qLength)) return 0;
if (!(in >> alignment.qPos)) return 0;
if (!(in >> qEnd)) return 0;
if (!(in >> qStrand)) return 0;
if (!(in >> alignment.tName)) return 0;
if (!(in >> tLength)) return 0;
if (!(in >> alignment.tPos)) return 0;
if (!(in >> tEnd)) return 0;
if (!(in >> tStrand)) return 0;
if (!(in >> alignment.score)) return 0;
if (!(in >> alignment.nMatch)) return 0;
if (!(in >> alignment.nMismatch)) return 0;
if (!(in >> alignment.nIns)) return 0;
if (!(in >> alignment.nDel)) return 0;
return 1;
}
template<typename T_Alignment>
inline int ReadCompSeqAlignment(std::istream &in, T_Alignment &alignment) {
if (!ReadCompareSequencesAlignmentStats(in, alignment)) return 0;
std::string alignStr;
if (!(in >> alignment.qString)) return 0;
if (!(in >> alignStr)) return 0;
if (!(in >> alignment.tString)) return 0;
std::string eol;
std::getline(in, eol);
return 1;
}
template<typename T_QuerySequence, typename T_TargetSequence>
void AppendGapCharacters(Gap &gap,
T_QuerySequence &query, T_TargetSequence &text,
DNALength &q, DNALength &t,
char mismatchChar, char gapChar,
std::string &textStr, std::string &alignStr, std::string &queryStr) {
int gp;
for (gp = 0; gp < gap.length; gp++) {
if (gap.seq == Gap::Query) {
textStr.push_back(text[t]);
alignStr.push_back(mismatchChar);
queryStr.push_back(gapChar);
t++;
}
else if (gap.seq == Gap::Target) {
textStr.push_back(gapChar);
alignStr.push_back(mismatchChar);
queryStr.push_back(query[q]);
q++;
}
}
}
template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
void CreateAlignmentStrings(T_Alignment &alignment,
T_QuerySequence &query, T_TargetSequence &text,
std::string &textStr, std::string &alignStr, std::string &queryStr,
DNALength queryLength, DNALength textLength) {
DNALength q = alignment.qPos;
DNALength t = alignment.tPos;
DNALength qPos, tPos;
DNALength g;
char mismatchChar = '*';
char matchChar = '|';
char gapChar = '-';
char gapSeparationChar = ' ';
if (alignment.blocks.size() == 0) {
textStr = "";
alignStr = "";
queryStr = "";
return;
}
if (alignment.gaps.size() == 0) {
//
// If there is no gap list, add the gaps as an offset here.
//
if (alignment.blocks[0].qPos > 0 or
alignment.blocks[0].tPos > 0) {
// commonGapLen should be the shorter gap.
qPos = alignment.blocks[0].qPos;
tPos = alignment.blocks[0].tPos;
DNALength commonGapLen = qPos;
if (commonGapLen > tPos) {
commonGapLen = tPos;
}
for (g = 0; g < commonGapLen; g++ ) {
textStr.push_back(text[t]);
alignStr.push_back(mismatchChar);
queryStr.push_back(query[q]);
t++;
q++;
}
tPos -= commonGapLen;
qPos -= commonGapLen;
//
// one of tPos or qPos is now 0.
// The other represents extra sequence
// that should be output before starting the alignment
DNALength p;
for (p = 0; p < tPos; p++) {
textStr.push_back(text[t]);
alignStr.push_back(gapSeparationChar);
queryStr.push_back(gapChar);
t++;
}
for (p = 0; p < qPos; p++) {
textStr.push_back(gapChar);
alignStr.push_back(gapSeparationChar);
queryStr.push_back(query[q]);
q++;
}
}
}
//
// Add gap characters if they are before the beginning of the alignment.
// This shouldn't happen, but for some local alignments, it can.
//
DNALength b, bl, gi;
if (alignment.gaps.size() > 0) {
// The first gap is before the first block of characters.
DNALength gi;
for (gi = 0; gi < alignment.gaps[0].size(); gi++) {
AppendGapCharacters(alignment.gaps[0][gi], query, text, q, t, mismatchChar, gapChar, textStr, alignStr, queryStr);
}
}
for (b = 0; b < alignment.size() ; b++) {
for (bl = 0; bl < alignment.blocks[b].length; bl++ ) {
queryStr.push_back(query[q]);
textStr.push_back(text[t]);
assert(queryLength == 0 or q < queryLength);
assert(textLength == 0 or t < textLength);
if (TwoBit[query[q]] !=
TwoBit[text[t]])
alignStr.push_back(mismatchChar);
else
alignStr.push_back(matchChar);
q++;
t++;
}
//
// There are no gaps to count after the last block, so
// don't add the gapped characters for this.
//
if (alignment.blocks.size() == 0)
continue;
if (b == alignment.blocks.size() - 1) {
continue;
}
if (alignment.gaps.size() > 0) {
for (gi = 0; gi < alignment.gaps[b+1].size(); gi++) {
AppendGapCharacters(alignment.gaps[b+1][gi], query, text, q, t, gapSeparationChar, gapChar, textStr, alignStr, queryStr);
}
}
else {
DNALength queryGapLen = (alignment.blocks[b+1].qPos -
alignment.blocks[b].qPos - alignment.blocks[b].length);
DNALength textGapLen = (alignment.blocks[b+1].tPos -
alignment.blocks[b].tPos - alignment.blocks[b].length);
if (queryGapLen > 0 or textGapLen > 0) {
// commonGapLen should be the shorter gap.
DNALength commonGapLen = queryGapLen;
if (queryGapLen > textGapLen) {
commonGapLen = textGapLen;
}
textGapLen -= commonGapLen;
queryGapLen -= commonGapLen;
for (g = 0; g < queryGapLen; g++, q++ ){
textStr.push_back(gapChar);
alignStr.push_back(gapSeparationChar);
queryStr.push_back(query[q]);
}
for (g = 0; g < textGapLen; g++, t++ ){
textStr.push_back(text[t]);
alignStr.push_back(gapSeparationChar);
queryStr.push_back(gapChar);
}
for (g = 0; g < commonGapLen; g++ ) {
textStr.push_back(text[t]);
alignStr.push_back(gapSeparationChar);
queryStr.push_back(query[q]);
t++;
q++;
}
}
}
}
}
template<typename T_Alignment, typename T_ScoreFn>
void ComputeAlignmentStats(T_Alignment & alignment, Nucleotide* qSeq, Nucleotide * tSeq, T_ScoreFn & scoreFn, bool useAffineScore) {
(void)(useAffineScore);
int qp = 0, tp = 0;
int nMatch = 0, nMismatch = 0, nIns =0, nDel = 0;
float pctSimilarity;
std::string textStr, alignStr, queryStr;
CreateAlignmentStrings(alignment, qSeq, tSeq, textStr, alignStr, queryStr);
int i;
int alignLength = textStr.size();
for (i = 0; i < alignLength; i++ ) {
if ((textStr[i] != '-') and (queryStr[i] != '-')) {
int ti = (int)textStr[i];
int qi = (int)queryStr[i];
if (ThreeBit[ti] == ThreeBit[qi]) {
nMatch++;
}
else {
nMismatch++;
}
tp++;
qp++;
}
else if (textStr[i] == '-' and queryStr[i] != '-') {
nIns++;
qp++;
}
else if (queryStr[i] == '-' and textStr[i] != '-') {
nDel++;
tp++;
}
}
if (tp + qp > 0) {
if (textStr.size() + queryStr.size() > 0) {
pctSimilarity = (nMatch*2.0) / (textStr.size() + queryStr.size()) * 100;
}
else {
pctSimilarity = 0;
}
}
else {
pctSimilarity = 0;
}
alignment.score = ComputeAlignmentScore(queryStr, textStr, scoreFn);
alignment.nMatch = nMatch;
alignment.nMismatch = nMismatch;
alignment.nDel = nDel;
alignment.nIns = nIns;
alignment.pctSimilarity = pctSimilarity;
}
template<typename T_Alignment>
void ComputeAlignmentStats(T_Alignment &alignment, Nucleotide* qSeq, Nucleotide *tSeq, int matchMatrix[5][5], int ins, int del) {
DistanceMatrixScoreFunction<DNASequence, DNASequence> scoreFn(matchMatrix, ins, del);
ComputeAlignmentStats(alignment, qSeq, tSeq, scoreFn);
}
template<typename T_Alignment>
int ComputeDrift(T_Alignment &alignment) {
VectorIndex b;
int drift = 0;
int maxDrift = 0;
int driftBetweenBlocks;
if (alignment.blocks.size() == 0)
return 0;
for (b = 0; b < alignment.blocks.size() - 1; b++) {
driftBetweenBlocks = ComputeDrift(alignment.blocks[b], alignment.blocks[b+1]);
drift += driftBetweenBlocks;
if (abs(drift) > maxDrift)
maxDrift = abs(drift);
}
return maxDrift;
}
template<typename T_Alignment>
void RemoveAlignmentPrefixGaps(T_Alignment &alignment) {
if (alignment.gaps.size() == 0) {
return;
}
unsigned int g;
int tStart = 0, qStart = 0;
for (g = 0; g < alignment.gaps[0].size(); g++) {
if (alignment.gaps[0][g].seq == Gap::Target) {
qStart += alignment.gaps[0][g].length;
}
else if (alignment.gaps[0][g].seq == Gap::Query) {
tStart += alignment.gaps[0][g].length;
}
}
int b;
int nBlocks;
for (b = 0, nBlocks = alignment.blocks.size(); b < nBlocks; b++) {
alignment.blocks[b].qPos -= qStart;
alignment.blocks[b].tPos -= tStart;
}
alignment.gaps[0].clear();
alignment.tPos += tStart;
alignment.qPos += qStart;
}
template<typename T>
void QVsToCmpH5QVs(const std::string &qvs,
const std::vector<unsigned char> &byteAlignment,
bool isTag,
std::vector<T> *gappedQVs) {
gappedQVs->clear();
unsigned int qv_i = 0;
// QVs and tags get different values at gaps in the read
char tagGapChar = 'N';
UChar qvGapChar = 255;
for (unsigned i=0; i<byteAlignment.size(); i++) {
if (byteAlignment[i] >> 4 == 0) { //Look at upper bits to get query char
if (isTag) {
gappedQVs->push_back(tagGapChar);
} else {
gappedQVs->push_back(qvGapChar);
}
} else {
if (isTag) {
//std::cout << "Pushing back " << (T)qvs[qv_i] << " for tag " << qvs[qv_i] << std::endl;
gappedQVs->push_back((T)qvs[qv_i]);
} else {
//std::cout << "Pushing back " << (T)qvs[qv_i] - FASTQSequence::charToQuality << " for QV " << qvs[qv_i] << std::endl;
gappedQVs->push_back((T)qvs[qv_i] - FASTQSequence::charToQuality);
}
qv_i++;
}
}
assert(gappedQVs->size() == byteAlignment.size());
}
#endif
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