/usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.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_SDP_ALIGN_IMPL_HPP_
#include <cstddef>
#include <vector>
#include <math.h>
#include <cstdlib>
#include <ostream>
// pbdata
#include "../../../pbdata/Types.h"
#include "../../../pbdata/defs.h"
#include "../../../pbdata/utils.hpp"
#include "../../../pbdata/Enumerations.h"
#include "../../../pbdata/DNASequence.hpp"
#include "../../../pbdata/matrix/FlatMatrix.hpp"
#include "../../datastructures/alignment/Alignment.hpp"
#include "GraphPaper.hpp"
#include "AlignmentUtils.hpp"
#include "SWAlign.hpp"
#include "sdp/SDPFragment.hpp"
#include "sdp/SparseDynamicProgramming.hpp"
#include "SDPAlign.hpp"
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
T_ScoreFn &scoreFn, int wordSize,
int sdpIns, int sdpDel, float indelRate,
blasr::Alignment &alignment,
AlignmentType alignType,
bool detailedAlignment,
bool extendFrontByLocalAlignment,
DNALength noRecurseUnder,
bool fastSDP,
unsigned int minFragmentsToUseGraphPaper) {
/*
Since SDP Align uses a large list of buffers, but none are
provided with this mechanism of calling SDPAlign, allocate the
buffers on the stack.
*/
std::vector<Fragment> fragmentSet, prefixFragmentSet, suffixFragmentSet;
TupleList<PositionDNATuple> targetTupleList;
TupleList<PositionDNATuple> targetPrefixTupleList;
TupleList<PositionDNATuple> targetSuffixTupleList;
std::vector<int> maxFragmentChain;
return SDPAlign(query, target,
scoreFn, wordSize,
sdpIns, sdpDel, indelRate,
alignment,
fragmentSet, prefixFragmentSet, suffixFragmentSet,
targetTupleList, targetPrefixTupleList, targetSuffixTupleList,
maxFragmentChain,
alignType,
detailedAlignment,
extendFrontByLocalAlignment,
noRecurseUnder,
fastSDP,
minFragmentsToUseGraphPaper);
}
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_BufferCache>
int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
T_ScoreFn &scoreFn, int wordSize,
int sdpIns, int sdpDel, float indelRate,
blasr::Alignment &alignment,
T_BufferCache &buffers,
AlignmentType alignType,
bool detailedAlignment,
bool extendFrontByLocalAlignment,
DNALength noRecurseUnder,
bool fastSDP,
unsigned int minFragmentsToUseGraphPaper) {
return SDPAlign(query, target, scoreFn, wordSize,
sdpIns, sdpDel, indelRate,
alignment,
buffers.sdpFragmentSet,
buffers.sdpPrefixFragmentSet,
buffers.sdpSuffixFragmentSet,
buffers.sdpCachedTargetTupleList,
buffers.sdpCachedTargetPrefixTupleList,
buffers.sdpCachedTargetSuffixTupleList,
buffers.sdpCachedMaxFragmentChain,
alignType, detailedAlignment,
extendFrontByLocalAlignment, noRecurseUnder,
fastSDP, minFragmentsToUseGraphPaper);
}
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_TupleList>
int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
T_ScoreFn &scoreFn,
int wordSize,
int sdpIns, int sdpDel, float indelRate,
blasr::Alignment &alignment,
std::vector<Fragment> &fragmentSet,
std::vector<Fragment> &prefixFragmentSet,
std::vector<Fragment> &suffixFragmentSet,
T_TupleList &targetTupleList,
T_TupleList &targetPrefixTupleList,
T_TupleList &targetSuffixTupleList,
std::vector<int> &maxFragmentChain,
// A few optinal parameters, should delete that last one.
AlignmentType alignType,
bool detailedAlignment,
bool extendFrontByLocalAlignment,
DNALength noRecurseUnder,
bool fastSDP,
unsigned int minFragmentsToUseGraphPaper) {
// minFragmentsToUseGraphPaper: minimum number of fragments to
// use Graph Paper for speed up.
fragmentSet.clear();
prefixFragmentSet.clear();
suffixFragmentSet.clear();
targetTupleList.clear();
targetPrefixTupleList.clear();
targetSuffixTupleList.clear();
maxFragmentChain.clear();
//
// Collect a set of matching fragments between query and target.
// Since this function is an inner-loop for alignment, anything to
// speed it up will help. One way to speed it up is to re-use the
// vectors that contain the sdp matches.
//
TupleMetrics tm, tmSmall;
tm.Initialize(wordSize);
int smallWordSize = (wordSize < SDP_DETAILED_WORD_SIZE ? wordSize : SDP_DETAILED_WORD_SIZE);
tmSmall.Initialize(smallWordSize);
//
// Partition the read into a prefix, middle, and suffix. The prefix
// and suffix are matched using a smaller word size allowing for
// higher sensitivity at the ends of reads, which are more likely to
// be misaligned.
//
int prefixLength, middleLength, suffixLength, suffixPos; // prefix pos is 0
prefixLength = min(target.length, (DNALength) SDP_PREFIX_LENGTH);
suffixLength = min(target.length - prefixLength, (DNALength) SDP_SUFFIX_LENGTH);
middleLength = target.length - prefixLength - suffixLength;
DNASequence prefix, middle, suffix;
DNASequence qPrefix, qMiddle, qSuffix;
DNALength pos = 0;
prefix.seq = &target.seq[pos];
prefix.length = prefixLength;
pos += prefixLength;
// Align the entire query against the entire target to get alignments
// in the middle.
middle.seq = &target.seq[0];
middle.length = target.length;
pos += middleLength;
suffixPos = pos; // while = prefixLength + middleLength
suffix.seq = &target.seq[suffixPos];
suffix.length = suffixLength;
int qPrefixLength, qMiddleLength, qSuffixLength, qMiddlePos, qSuffixPos; // prefix pos is 0
qPrefixLength = min(query.length, (DNALength) SDP_PREFIX_LENGTH);
qSuffixLength = min(query.length - qPrefixLength, (DNALength) SDP_SUFFIX_LENGTH);
qMiddleLength = query.length - qPrefixLength - qSuffixLength;
pos = 0;
qPrefix.seq = &query.seq[pos];
qPrefix.length = qPrefixLength;
// Align the entire query against the entire target to get alignments
// in the middle.
qMiddle.seq = &query.seq[0];
qMiddle.length = query.length;
qMiddlePos = pos += qPrefixLength;
(void)(qMiddlePos);
qSuffixPos = pos += qMiddleLength; // = qPrefixLength + qMiddleLength
qSuffix.seq = &query.seq[qSuffixPos];
qSuffix.length = qSuffixLength;
fragmentSet.clear();
SequenceToTupleList(prefix, tmSmall, targetPrefixTupleList);
SequenceToTupleList(suffix, tmSmall, targetSuffixTupleList);
SequenceToTupleList(middle, tm, targetTupleList);
targetPrefixTupleList.Sort();
targetSuffixTupleList.Sort();
targetTupleList.Sort();
//
// Store in fragmentSet the tuples that match between the target
// and query.
//
StoreMatchingPositions(qPrefix, tmSmall, targetPrefixTupleList, prefixFragmentSet);
StoreMatchingPositions(qSuffix, tmSmall, targetSuffixTupleList, suffixFragmentSet);
StoreMatchingPositions(qMiddle, tm, targetTupleList, fragmentSet);
//
// The method to store matching positions is not weight aware.
// Store the weight here.
//
VectorIndex f;
for (f = 0; f < suffixFragmentSet.size(); f++) {
(suffixFragmentSet)[f].weight = tm.tupleSize;
(suffixFragmentSet)[f].length = tmSmall.tupleSize;
}
for (f = 0; f < prefixFragmentSet.size(); f++) {
(prefixFragmentSet)[f].weight = tm.tupleSize;
(prefixFragmentSet)[f].length = tmSmall.tupleSize;
}
for (f = 0; f < fragmentSet.size(); f++) {
(fragmentSet)[f].weight = tm.tupleSize;
(fragmentSet)[f].length = tm.tupleSize;
}
//
// Since different partitions of the read are matched, the locations
// of the matches do not have the correct position because of the
// offsets. Fix that here.
for (f = 0; f < suffixFragmentSet.size(); f++) {
(suffixFragmentSet)[f].x += qSuffixPos;
(suffixFragmentSet)[f].y += suffixPos;
}
//
// Collect all fragments into one.
//
fragmentSet.insert(fragmentSet.begin(), prefixFragmentSet.begin(), prefixFragmentSet.end());
fragmentSet.insert(fragmentSet.end(), suffixFragmentSet.begin(), suffixFragmentSet.end());
FlatMatrix2D<int> graphScoreMat;
FlatMatrix2D<Arrow> graphPathMat;
FlatMatrix2D<int> graphBins;
if (fragmentSet.size() > minFragmentsToUseGraphPaper and fastSDP) {
int nCol = 50;
vector<bool> onOptPath(fragmentSet.size(), false);
GraphPaper<Fragment>(fragmentSet, nCol, nCol,
graphBins, graphScoreMat,
graphPathMat, onOptPath);
RemoveOffOpt(fragmentSet, onOptPath);
}
graphScoreMat.Clear();
graphPathMat.Clear();
graphBins.Clear();
//
// Because there are fragments from multiple overlapping regions, remove
// any fragments that have the same starting coordinate as a
// previous fragment.
//
std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<Fragment>());
f = 0;
int fCur = 0;
while (f + 1 <= fragmentSet.size()) {
fragmentSet[fCur] = fragmentSet[f];
while (f < fragmentSet.size() and fragmentSet[fCur].x == fragmentSet[f].x and fragmentSet[fCur].y == fragmentSet[f].y) {
f++;
}
fCur++;
}
fragmentSet.resize(fCur);
if (fragmentSet.size() == 0) {
//
// This requires at least one seeded tuple to begin an alignment.
//
return 0;
}
//
// Find the longest chain of anchors.
//
SDPLongestCommonSubsequence(query.length, fragmentSet, tm.tupleSize, sdpIns, sdpDel, scoreFn.scoreMatrix[0][0], maxFragmentChain, alignType);
//
// Now turn the max fragment chain into a real alignment.
//
int startF;
blasr::Alignment chainAlignment;
alignment.qPos = 0;
alignment.tPos = 0;
Block block;
std::vector<int> fragScoreMat;
std::vector<Arrow> fragPathMat;
//
// Patch the sdp fragments into an alignment, possibly breaking the
// alignment if the gap between two fragments is too large.
//
for (f = 0; f < maxFragmentChain.size(); f++ ){
startF = f;
// Condense contiguous stretches.
while(f < maxFragmentChain.size() - 1 and
fragmentSet[maxFragmentChain[f]].x == fragmentSet[maxFragmentChain[f+1]].x - 1 and
fragmentSet[maxFragmentChain[f]].y == fragmentSet[maxFragmentChain[f+1]].y - 1) {
f++;
}
block.qPos = fragmentSet[maxFragmentChain[startF]].x;
block.tPos = fragmentSet[maxFragmentChain[startF]].y;
// Compute the block length as the difference between the starting
// point of the current block and ending point of the last
// overlapping block. This was previously calculated by adding
// the number of merged blocks - 1 to the first block length.
// When the block lengths are heterogenous, this does not work,
// and it would be possible to have a block with a length that
// extends past the end of a sequence. By taking the length as
// the difference here, it ensures this will not happen.
//
block.length = fragmentSet[maxFragmentChain[f]].x + fragmentSet[maxFragmentChain[f]].length - fragmentSet[maxFragmentChain[startF]].x;
chainAlignment.blocks.push_back(block);
}
//
// It may be possible that in regions of low similarity, spurious matches fit into the LCS.
// Assume that indels cause the matches to diverge from the diagonal on a random walk. If they
// walk more than 3 standard deviations away from the diagonal, they are probably spurious.
//
unsigned int b;
chainAlignment.qPos = 0;
chainAlignment.tPos = 0;
for (b = 0; b < chainAlignment.size()-1; b++){
if (chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length > chainAlignment.blocks[b+1].qPos) {
chainAlignment.blocks[b].length = (chainAlignment.blocks[b+1].qPos - chainAlignment.blocks[b].qPos);
}
if (chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length > chainAlignment.blocks[b+1].tPos) {
chainAlignment.blocks[b].length = (chainAlignment.blocks[b+1].tPos - chainAlignment.blocks[b].tPos);
}
// the min indel rate between the two chain blocks is the difference in diagonals between the two sequences.
int curDiag, nextDiag, diffDiag;
curDiag = chainAlignment.blocks[b].tPos - chainAlignment.blocks[b].qPos;
nextDiag = chainAlignment.blocks[b+1].tPos - chainAlignment.blocks[b+1].qPos;
diffDiag = std::abs(curDiag - nextDiag);
//
// It is expected that the deviation is at least 1, so discount for this
//
diffDiag--;
// compare the alignment distances.
}
std::vector<bool> blockIsGood;
blockIsGood.resize(chainAlignment.size());
fill(blockIsGood.begin(), blockIsGood.end(), true);
//
// The hack that allows anchors of different lengths at the front
// and end of alignments (to increase sensitivity at the ends of
// sequences) has the side effect that there may be blocks that have
// zero length. This shouldn't happen, so to balance this out
// remove blocks that have zero length.
//
for (b = 0; b < chainAlignment.size(); b++){
if (chainAlignment.blocks[b].length == 0) {
blockIsGood[b] = false;
}
}
for (b = 1; b < chainAlignment.size()-1; b++){
// the min indel rate between the two chain blocks is the difference in diagonals between the two sequences.
int prevDiag = abs(((int)chainAlignment.blocks[b].tPos - (int)chainAlignment.blocks[b].qPos) -
((int)chainAlignment.blocks[b-1].tPos - (int)chainAlignment.blocks[b-1].qPos));
int prevDist = std::min(chainAlignment.blocks[b].tPos - chainAlignment.blocks[b-1].tPos,
chainAlignment.blocks[b].qPos - chainAlignment.blocks[b-1].qPos);
int nextDiag = abs(((int)chainAlignment.blocks[b+1].tPos - (int)chainAlignment.blocks[b+1].qPos) -
((int)chainAlignment.blocks[b].tPos - (int)chainAlignment.blocks[b].qPos));
int nextDist = std::min(chainAlignment.blocks[b+1].tPos - chainAlignment.blocks[b].tPos,
chainAlignment.blocks[b+1].qPos - chainAlignment.blocks[b].qPos);
if (prevDist * indelRate < prevDiag and nextDist * indelRate < nextDiag) {
blockIsGood[b] = false;
}
}
for (b = chainAlignment.size(); b > 0; b--) {
if (blockIsGood[b-1] == false) {
chainAlignment.blocks.erase(chainAlignment.blocks.begin() + b-1);
}
}
if (chainAlignment.blocks.size() > 0) {
T_QuerySequence qFragment;
T_TargetSequence tFragment;
blasr::Alignment fragAlignment;
unsigned int fb;
if (alignType == Global) {
//
// For Global alignment, refine the alignment from the beginnings of the
// sequences to the start of the first block.
//
if (chainAlignment.blocks[0].qPos > 0 and
chainAlignment.blocks[0].tPos > 0) {
qFragment.seq = &query.seq[0];
qFragment.length = chainAlignment.blocks[0].qPos;
tFragment.seq = &target.seq[0];
tFragment.length = chainAlignment.blocks[0].tPos;
for (fb = 0; fb < alignment.blocks.size(); fb++) {
alignment.blocks.push_back(fragAlignment.blocks[b]);
}
}
}
else if (alignType == Local) {
// Perform a front-anchored alignment to extend the alignment to
// the beginning of the read.
if (chainAlignment.blocks[0].qPos > 0 and
chainAlignment.blocks[0].tPos > 0) {
qFragment.seq = (Nucleotide*) &query.seq[0];
qFragment.length = chainAlignment.blocks[0].qPos;
tFragment.seq = (Nucleotide*) &target.seq[0];
tFragment.length = chainAlignment.blocks[0].tPos;
blasr::Alignment frontAlignment;
// Currently, there might be some space between the beginning
// of the alignment and the beginning of the read. Run an
// EndAnchored alignment that allows free gaps to the start of
// where the alignment begins, but normal, ungapped alignment
// otherwise.
if (extendFrontByLocalAlignment) {
if (noRecurseUnder == 0 or qFragment.length * tFragment.length < noRecurseUnder) {
SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, frontAlignment, scoreFn, EndAnchored);
} else {
// cout << "running recursive sdp alignment. " << endl;
vector<int> recurseFragmentChain;
SDPAlign(qFragment, tFragment, scoreFn,
std::max(wordSize/2, 5),
sdpIns, sdpDel, indelRate,
frontAlignment,
fragmentSet,
prefixFragmentSet,
suffixFragmentSet,
targetTupleList,
targetPrefixTupleList,
targetSuffixTupleList,
recurseFragmentChain,
alignType, detailedAlignment,
extendFrontByLocalAlignment, 0);
}
unsigned int anchorBlock;
for (anchorBlock = 0; anchorBlock < frontAlignment.blocks.size(); anchorBlock++) {
//
// The front alignment needs to be transformed to the
// coordinate offsets that the chain alignment is in. This
// is an alignment starting at position 0 in the target and
// query. Currently, the front alignment is offset into the
// sequences by frontAlignment.[q/t]Pos.
//
frontAlignment.blocks[anchorBlock].tPos += frontAlignment.tPos;
frontAlignment.blocks[anchorBlock].qPos += frontAlignment.qPos;
alignment.blocks.push_back(frontAlignment.blocks[anchorBlock]);
}
}
}
}
//
// The chain alignment blocks are not complete blocks, so they
// must be appended to the true alignment and then patched up.
//
for (b = 0; b < chainAlignment.size() - 1; b++) {
alignment.blocks.push_back(chainAlignment.blocks[b]);
//
// Do a detaied smith-waterman alignment between blocks, if this
// is specified.
fragAlignment.Clear();
qFragment.Free();
qFragment.ReferenceSubstring(query, chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length);
qFragment.length = chainAlignment.blocks[b+1].qPos -
(chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length);
tFragment.seq = &(target.seq[chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length]);
tFragment.length = (chainAlignment.blocks[b+1].tPos -
(chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length));
if (qFragment.length > 0 and
tFragment.length > 0 and
detailedAlignment == true) {
if (noRecurseUnder == 0 or qFragment.length * tFragment.length < noRecurseUnder) {
SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, fragAlignment, scoreFn, Global);
}
else {
// cout << "running recursive sdp alignment on " << qFragment.length * tFragment.length << endl;
std::vector<int> recurseFragmentChain;
SDPAlign(qFragment, tFragment, scoreFn,
std::max(wordSize/2, 5),
sdpIns, sdpDel, indelRate,
fragAlignment,
fragmentSet,
prefixFragmentSet,
suffixFragmentSet,
targetTupleList,
targetPrefixTupleList,
targetSuffixTupleList,
recurseFragmentChain,
alignType, detailedAlignment, 0, 0);
}
fragAlignment.qPos = 0;
fragAlignment.tPos = 0;
int qOffset = chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length;
int tOffset = chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length;
for (fb = 0; fb < fragAlignment.blocks.size(); fb++) {
fragAlignment.blocks[fb].qPos += qOffset;
fragAlignment.blocks[fb].tPos += tOffset;
alignment.blocks.push_back(fragAlignment.blocks[fb]);
}
}
}
int lastBlock = chainAlignment.blocks.size() - 1;
if (alignType == Global or alignType == Local) {
if (chainAlignment.size() > 0) {
// Add the last block.
alignment.blocks.push_back(chainAlignment.blocks[lastBlock]);
if (alignType == Global and detailedAlignment == true) {
//
// When doing a global alignment, the sequence from the end of
// the last block of the query should be aligned to the end of
// the text.
//
qFragment.Free();
qFragment.ReferenceSubstring(query, chainAlignment.blocks[lastBlock].qPos + chainAlignment.blocks[lastBlock].length,
query.length -
(chainAlignment.blocks[lastBlock].qPos + chainAlignment.blocks[lastBlock].length));
tFragment.seq = &(target.seq[chainAlignment.blocks[lastBlock].tPos + chainAlignment.blocks[lastBlock].length]);
tFragment.length = (target.length -
(chainAlignment.blocks[lastBlock].tPos + chainAlignment.blocks[lastBlock].length));
if (qFragment.length > 0 and
tFragment.length > 0 ) {
if (extendFrontByLocalAlignment) {
fragAlignment.Clear();
if (qFragment.length * tFragment.length > 10000) {
// cout << "Cautin: slow alignment crossing! " << qFragment.length << " " << tFragment.length << endl;
}
if (noRecurseUnder == 0 or qFragment.length * tFragment.length < noRecurseUnder) {
SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, fragAlignment, scoreFn, EndAnchored);
}
else {
std::vector<int> recurseFragmentChain;
SDPAlign(qFragment, tFragment, scoreFn,
std::max(wordSize/2, 5),
sdpIns, sdpDel, indelRate,
fragAlignment,
fragmentSet,
prefixFragmentSet,
suffixFragmentSet,
targetTupleList,
targetPrefixTupleList,
targetSuffixTupleList,
recurseFragmentChain,
alignType, detailedAlignment, extendFrontByLocalAlignment, 0);
}
int qOffset = chainAlignment.blocks[lastBlock].qPos + chainAlignment.blocks[lastBlock].length;
int tOffset = chainAlignment.blocks[lastBlock].tPos + chainAlignment.blocks[lastBlock].length;
unsigned int fb;
for (fb = 0; fb < fragAlignment.size(); fb++) {
fragAlignment.blocks[fb].qPos += qOffset;
fragAlignment.blocks[fb].tPos += tOffset;
alignment.blocks.push_back(fragAlignment.blocks[fb]);
}
}
}
}
}
}
}
if (alignType == Local) {
alignment.tPos = alignment.blocks[0].tPos;
alignment.qPos = alignment.blocks[0].qPos;
VectorIndex b;
for (b = 0; b < alignment.blocks.size(); b++) {
alignment.blocks[b].qPos -= alignment.qPos;
alignment.blocks[b].tPos -= alignment.tPos;
}
}
int alignmentScore;
/* ofstream queryOut("query.fasta");
FASTASequence tmp;
((DNASequence&)tmp).Copy(query);
tmp.CopyTitle("query");
tmp.PrintSeq(queryOut);
queryOut.close();
ofstream targetOut("target.fasta");
((DNASequence&)tmp).Copy(target);
tmp.CopyTitle("target");
tmp.PrintSeq(targetOut);
targetOut.close();
*/
alignmentScore = ComputeAlignmentScore(alignment, query, target, scoreFn);
return alignmentScore;
}
#endif //_BLASR_SDP_ALIGN_IMPL_HPP_
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