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LocalRefineAlignment.h
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#ifndef LOCAL_REFINE_ALIGNMENT_H
#define LOCAL_REFINE_ALIGNMENT_H
#include <math.h>
#include "MMIndex.h"
#include "Genome.h"
#include "Read.h"
#include "Options.h"
#include "CompareLists.h"
#include "Sorting.h"
#include "TupleOps.h"
#include "Clustering.h"
#include "AffineOneGapAlign.h"
// #include "GlobalChain.h"
#include "TupleOps.h"
#include "SparseDP.h"
#include "SparseDP_Forward.h"
#include "Chain.h"
#include "overload.h"
#include "LinearExtend.h"
#include "SplitClusters.h"
#include "Timing.h"
#include "ClusterRefine.h"
#include <iostream>
#include <algorithm>
#include <iterator>
#include <ctime>
#include <cmath> // std::log
#include <sstream>
#include <thread>
#include <climits>
#include <map>
//
// This function seperates finalchain by different strands;
//
void debug_alignment (Alignment *alignment, int readlength, int genomeLen) {
// This is for debugging
if (alignment->blocks.size() > 1) {
int last=alignment->blocks.size();
assert(alignment->blocks[last-2].qPos + alignment->blocks[last-2].length < readlength);
assert(alignment->blocks[last-2].tPos + alignment->blocks[last-2].length < genomeLen);
assert(alignment->blocks[last-2].qPos + alignment->blocks[last-2].length <= alignment->blocks[last-1].qPos);
assert(alignment->blocks[last-2].tPos + alignment->blocks[last-2].length <= alignment->blocks[last-1].tPos);
}
}
void
SeparateChainByStrand(UltimateChain & chain, vector<vector<int>> & finalSeperateChain) {
vector<int> sep;
int fl = 0;
sep.push_back(fl);
while (fl < chain.size() - 1) {
if (chain.strand(fl) == chain.strand(fl+1)) {
fl++;
}
else {
sep.push_back(fl+1);
finalSeperateChain.push_back(sep);
sep.clear();
sep.push_back(fl+1);
fl++;
}
}
if (fl == chain.size() - 1) {
sep.push_back(fl+1);
finalSeperateChain.push_back(sep);
}
}
int
LargestFinalSeperateChain(vector<vector<int>> &finalSeperateChain) {
int maxi = 0;
for (int mi = 1; mi < finalSeperateChain.size(); mi++) {
if (finalSeperateChain[mi].back() - finalSeperateChain[mi][0] > finalSeperateChain[maxi].back() - finalSeperateChain[maxi][0]){
maxi = mi;
}
}
return maxi;
}
int
PassgenomeThres(int cur, GenomePos & genomeThres, UltimateChain & ultimatechain) {
if (genomeThres != 0 and ultimatechain[cur].second.pos < genomeThres) return 1;
else return 0;
}
int
Matched(GenomePos qs, GenomePos qe, GenomePos ts, GenomePos te) {
return min(qe-qs+1, te-ts+1); // TODO(Jingwen): check whether should add 1
}
void
SetMatchAndGaps(GenomePos qs, GenomePos qe, GenomePos ts, GenomePos te, int &m, int &qg, int &tg) {
m=Matched(qs, qe, ts, te);
qg=qe-qs+1-m; //TODO(Jingwen): check whether should add 1
tg=te-ts+1-m;
}
int
AlignSubstrings(char *qSeq, GenomePos &qStart, GenomePos &qEnd, char *tSeq, GenomePos &tStart, GenomePos &tEnd,
vector<int> &scoreMat, vector<Arrow> &pathMat, Alignment &aln, const Options &options,
AffineAlignBuffers &buff) {
int qLen = qEnd-qStart;
int tLen = tEnd-tStart;
int drift = abs(qLen - tLen);
int k = max(7, drift+1);
/*
int score = KBandAlign(&qSeq[qStart], qEnd-qStart, &tSeq[tStart], tEnd-tStart, -5,3,2,2, k, scoreMat, pathMat, aln);*/
string readSeq(&qSeq[qStart], qEnd-qStart);
string chromSeq(&tSeq[tStart],tEnd-tStart);
int score = AffineOneGapAlign(readSeq, qLen, chromSeq, tLen, options.localMatch, options.localMismatch, options.localIndel,
min(drift*2+1,options.localBand), aln, buff);
/*
cout << "aligned " << endl
<< readSeq << endl
<< chromSeq;
aln.genomeLen = chromSeq.size();
aln.read=(char*) readSeq.c_str();
aln.genome=(char*) chromSeq.c_str();
aln.CreateAlignmentStrings((char*) readSeq.c_str(), (char*)chromSeq.c_str(), aln.queryString, aln.alignString, aln.refString);
aln.prepared=true;
aln.PrintPairwise(cout);
cout << endl;
*/
return score;
}
void
RefineSubstrings(char *read, GenomePos readSubStart, GenomePos readSubEnd, char *genome, GenomePos genomeSubStart,
GenomePos genomeSubEnd, vector<int> &scoreMat, vector<Arrow> &pathMat, Alignment &aln, const Options &opts,
AffineAlignBuffers &buff) {
aln.blocks.clear();
AlignSubstrings(read, readSubStart, readSubEnd, genome, genomeSubStart, genomeSubEnd, scoreMat, pathMat, aln, opts, buff);
for (int b = 0; b < aln.blocks.size(); b++) {
aln.blocks[b].qPos += readSubStart;
aln.blocks[b].tPos += genomeSubStart;
}
}
void
RefineByLinearAlignment(GenomePos &btc_curReadEnd, GenomePos &btc_curGenomeEnd, GenomePos &btc_nextReadStart, GenomePos &btc_nextGenomeStart,
bool str, int chromIndex, Alignment * alignment, Read & read, Genome & genome, char *strands[2],
vector<int> & scoreMat, vector<Arrow> & pathMat, const Options & opts, AffineAlignBuffers &buff) {
//
// find small matches between fragments in gapChain
int m, rg, gg;
SetMatchAndGaps(btc_curReadEnd, btc_nextReadStart, btc_curGenomeEnd, btc_nextGenomeStart, m, rg, gg);
if (m > 0) {
Alignment betweenAnchorAlignment;
if (opts.refineLevel & REF_DP) {
RefineSubstrings(strands[str], btc_curReadEnd, btc_nextReadStart, genome.seqs[chromIndex],
btc_curGenomeEnd, btc_nextGenomeStart, scoreMat, pathMat, betweenAnchorAlignment, opts, buff);
int b;
// for (b = 1; b < betweenAnchorAlignment.blocks.size(); b++) {
// assert(betweenAnchorAlignment.blocks[b-1].qPos + betweenAnchorAlignment.blocks[b-1].length <= betweenAnchorAlignment.blocks[b].qPos);
// assert(betweenAnchorAlignment.blocks[b-1].tPos + betweenAnchorAlignment.blocks[b-1].length <= betweenAnchorAlignment.blocks[b].tPos);
// }
alignment->blocks.insert(alignment->blocks.end(), betweenAnchorAlignment.blocks.begin(), betweenAnchorAlignment.blocks.end());
if (opts.dotPlot and !opts.readname.empty() and read.name == opts.readname) {
ofstream Lclust("LinearAlignment.tab", std::ofstream::app);
for (b = 0; b < betweenAnchorAlignment.blocks.size(); b++) {
Lclust << betweenAnchorAlignment.blocks[b].qPos << "\t"
<< betweenAnchorAlignment.blocks[b].tPos + genome.header.pos[chromIndex]<< "\t"
<< betweenAnchorAlignment.blocks[b].qPos + betweenAnchorAlignment.blocks[b].length << "\t"
<< betweenAnchorAlignment.blocks[b].tPos + betweenAnchorAlignment.blocks[b].length + genome.header.pos[chromIndex]<< "\t"
<< str << endl;
}
Lclust.close();
}
// for (int bb = 1; bb < alignment->blocks.size(); bb++) {
// assert(alignment->blocks[bb-1].qPos + alignment->blocks[bb-1].length <= read.length);
// assert(alignment->blocks[bb-1].tPos + alignment->blocks[bb-1].length <= genome.lengths[chromIndex]);
// assert(alignment->blocks[bb-1].qPos + alignment->blocks[bb-1].length <= alignment->blocks[bb].qPos);
// assert(alignment->blocks[bb-1].tPos + alignment->blocks[bb-1].length <= alignment->blocks[bb].tPos);
// }
betweenAnchorAlignment.blocks.clear();
}
}
// genomeThres = 0;
}
void
SwitchToOriginalAnchors(FinalChain &prev, UltimateChain &cur, vector<Cluster_SameDiag *> &ExtendClusters, vector<Cluster> &extend_clusters) {
cur = UltimateChain(&extend_clusters, prev.SecondSDPValue);
for (int i = 0; i < prev.size(); i++) {
int c = prev.ClusterNum(i);
int k = prev.chain[i];
for (int j = ExtendClusters[c]->end[k] - 1; j >= ExtendClusters[c]->start[k]; j--) {
cur.chain.push_back(j);
cur.ClusterIndex.push_back(ExtendClusters[c]->coarse);
}
}
}
//
// This function creates the alignment for a "segment"(one big chunk) in the chain;
//
void
RefinedAlignmentbtwnAnchors(int cur, int next, bool str, bool inv_str, int &chromIndex, UltimateChain &chain, vector<SegAlignmentGroup> &alignments,
Alignment *alignment, Read &read, Genome &genome, char *strands[2], vector<int> &scoreMat,
vector<Arrow> &pathMat, Options tinyOpts, AffineAlignBuffers &buff,
const vector<float> & LookUpTable, bool &inversion, bool &breakalignment, ostream *svsigstrm) {
if (str == 0) alignment->blocks.push_back(Block(chain[cur].first.pos, chain[cur].second.pos, chain.length(cur)));
else {
alignment->blocks.push_back(Block(read.length - chain[cur].first.pos - chain.length(cur), chain[cur].second.pos, chain.length(cur)));
}
assert(chain[cur].first.pos + chain.length(cur) <= read.length);
assert(chain[cur].second.pos + chain.length(cur) <= genome.lengths[chromIndex]);
debug_alignment(alignment, read.length, genome.lengths[chromIndex]);
//
// Refine the alignment in the space between two adjacent anchors;
//
GenomePos curGenomeEnd, curReadEnd, nextGenomeStart, nextReadStart;
if (str == 0) {
curReadEnd = chain[cur].first.pos + chain.length(cur);
nextReadStart = chain[next].first.pos;
curGenomeEnd = chain[cur].second.pos + chain.length(cur);
nextGenomeStart = chain[next].second.pos;
}
else { // flip the space if it is reversed stranded
curReadEnd = read.length - chain[cur].first.pos;
nextReadStart = read.length - chain[next].first.pos - chain.length(next);
curGenomeEnd = chain[cur].second.pos + chain.length(cur);
nextGenomeStart = chain[next].second.pos;
}
assert(curReadEnd <= nextReadStart);
assert(nextReadStart <= read.length);
assert(nextGenomeStart <= genome.lengths[chromIndex]);
if (curGenomeEnd <= nextGenomeStart) {
long read_dist = nextReadStart - curReadEnd;
long genome_dist = nextGenomeStart - curGenomeEnd;
//
// The linear alignment is more suitable to find a big gap;
//
if (tinyOpts.RefineBySDP == true and min(read_dist, genome_dist) >= 300) {
GenomePairs *BtwnPairs;
GenomePairs for_BtwnPairs;
GenomePairs rev_BtwnPairs;
// cerr << "abs(read_dist-genome_dist): " << abs(read_dist-genome_dist)<< endl;
// cerr << "min(read_dist, genome_dist): " << min(read_dist, genome_dist) << endl;
// cerr << "curReadEnd: " << curReadEnd << " curGenomeEnd: " << curGenomeEnd << " nextReadStart: " << nextReadStart << " nextGenomeStart: " << nextGenomeStart << endl;
int refineSpaceDiag = 0;
//
// Create a diagonal band that is not too big, not too small
int sv_diag = max(read_dist, genome_dist) - min(read_dist, genome_dist);
if (tinyOpts.readType == Options::contig or tinyOpts.readType == Options::ccs ) {
refineSpaceDiag = min((int) floor(max(80.f, 0.01f * read_dist)), 500);
}
else if (tinyOpts.readType == Options::clr or tinyOpts.readType == Options::ont) {
refineSpaceDiag = min((int) floor(max(100.f, 0.15f * read_dist)), 2000);
}
refineSpaceDiag = max(2*sv_diag, refineSpaceDiag);
// int refineSpaceDiag = (int) (0.15f * read_dist);
float minRatio;
if (max(read_dist,genome_dist) < 100) {
tinyOpts.globalK = 6;
tinyOpts.localW = 5;
// Waiting time for a 6-mer with 85% accuracy=29.5
minRatio=0.5/29.5;
}
else if (max(read_dist,genome_dist) < 500) {
tinyOpts.globalK = 9;
tinyOpts.localW = 7;
// allow repetitive matches
tinyOpts.globalMaxFreq = 50;
tinyOpts.localMaxFreq = 50;
// Waiting time for a 9-mer with 85% accuracy=69.1
minRatio=0.5/69.1;
}
else {
tinyOpts.globalK = 12;
tinyOpts.localW = 7;
// Waitint time for a 12-mer with 85% accuracy=140.2
minRatio=0.5/140.2;
}
float identity=0;
identity = RefineSpace(tinyOpts.globalK, tinyOpts.localW, refineSpaceDiag, 0, for_BtwnPairs, tinyOpts, genome, read,
strands, chromIndex, nextReadStart, curReadEnd, nextGenomeStart, curGenomeEnd, str);
//
// If anchor is still too sparse, try finding seeds in the inversed direction
//
int minDist = min(read_dist, genome_dist);
// cout << "fbp " << for_BtwnPairs.size() << "\t" << for_BtwnPairs.size() / (float) minDist << "\t" << minRatio << "\t" << identity << endl;
if ((for_BtwnPairs.size() / (float) minDist) < minRatio and
alignments.back().SegAlignment.back()->blocks.size() >=5 and
identity < 0.8) { // try inversion
GenomePos temp = curReadEnd;
curReadEnd = read.length - nextReadStart;
nextReadStart = read.length - temp;
identity = RefineSpace(tinyOpts.globalK, tinyOpts.globalW, refineSpaceDiag, 0, rev_BtwnPairs, tinyOpts, genome, read, strands, chromIndex, nextReadStart, curReadEnd, nextGenomeStart, curGenomeEnd, inv_str);
// cout << "fbp " << rev_BtwnPairs.size() << "\t" << rev_BtwnPairs.size() / (float) minDist << "\t" << minRatio << "\t" << identity << endl;
double driftRate;
if (tinyOpts.readType == Options::contig or tinyOpts.readType == Options::ccs ) {
driftRate = 0.01f;
}
else if (tinyOpts.readType == Options::ont or tinyOpts.readType == Options::clr) {
driftRate = 0.10f;
}
// else {
// driftRate = 0.15f;
// }
if (for_BtwnPairs.size() == 0 and
rev_BtwnPairs.size() == 0 and
minDist > 500 and sv_diag <= max((double)50, minDist*driftRate)) {
// break the alignment; -- don't break easily
for_BtwnPairs.clear();
rev_BtwnPairs.clear();
breakalignment = 1;
inversion = 0;
return;
}
// if (rev_BtwnPairs.size() / (float) minDist < 0.005 and (for_BtwnPairs.size() / (float) minDist) < 0.005){
// // break the alignment; -- don't break easily
if (identity < 0.8 and
rev_BtwnPairs.size() / (float) minDist < minRatio){
// break the alignment;
for_BtwnPairs.clear();
rev_BtwnPairs.clear();
breakalignment = 1;
inversion = 0;
return;
}
if (for_BtwnPairs.size() >= rev_BtwnPairs.size()) {
BtwnPairs = &for_BtwnPairs;
rev_BtwnPairs.clear();
inversion = 0;
GenomePos temp = curReadEnd;
curReadEnd = read.length - nextReadStart;
nextReadStart = read.length - temp;
}
else {
BtwnPairs = &rev_BtwnPairs;
for_BtwnPairs.clear();
inversion = 1;
}
}
else {
BtwnPairs = &for_BtwnPairs;
}
if (BtwnPairs->size() > 0) {
GenomePairs ExtendBtwnPairs;
vector<int> ExtendBtwnPairsMatchesLength;
vector<unsigned int> BtwnChain;
LinearExtend(BtwnPairs, ExtendBtwnPairs, ExtendBtwnPairsMatchesLength, tinyOpts, genome, read, chromIndex, 0, 0, tinyOpts.globalK);
if (inversion == 0) {
//
// insert the next anchor;
//
ExtendBtwnPairs.push_back(GenomePair(GenomeTuple(0, nextReadStart), GenomeTuple(0, nextGenomeStart)));
ExtendBtwnPairsMatchesLength.push_back(chain.length(next));
//
// insert the previous anchor;
//
ExtendBtwnPairs.push_back(GenomePair(GenomeTuple(0, curReadEnd-chain.length(cur)), GenomeTuple(0, curGenomeEnd-chain.length(cur))));
ExtendBtwnPairsMatchesLength.push_back(chain.length(cur));
}
TrimOverlappedAnchors(ExtendBtwnPairs, ExtendBtwnPairsMatchesLength);
// nanoOpts.coefficient=12;//9 this is calibrately set to 12
float inv_value = 0; int inv_NumofAnchors = 0;
tinyOpts.freeGap=3;
SparseDP_ForwardOnly(ExtendBtwnPairs, ExtendBtwnPairsMatchesLength, BtwnChain, tinyOpts, LookUpTable, inv_value, inv_NumofAnchors, 2); //1
RemovePairedIndels(ExtendBtwnPairs, BtwnChain, ExtendBtwnPairsMatchesLength);
if (tinyOpts.dotPlot and read.name == tinyOpts.readname) {
ofstream pSclust("BtwnPairs.tab", std::ofstream::app);
for (int bp = BtwnPairs->size()-1; bp >= 0; bp--) {
if (inversion == 0) {
if (str == 0) {
pSclust << (*BtwnPairs)[bp].first.pos << "\t"
<< (*BtwnPairs)[bp].second.pos + genome.header.pos[chromIndex] << "\t"
<< (*BtwnPairs)[bp].first.pos + tinyOpts.globalK << "\t"
<< (*BtwnPairs)[bp].second.pos + tinyOpts.globalK + genome.header.pos[chromIndex] << "\t"
<< 0 << endl;
}
else if (str == 1) {
pSclust << read.length - (*BtwnPairs)[bp].first.pos - tinyOpts.globalK << "\t"
<< (*BtwnPairs)[bp].second.pos + tinyOpts.globalK + genome.header.pos[chromIndex]<< "\t"
<< read.length - (*BtwnPairs)[bp].first.pos << "\t"
<< (*BtwnPairs)[bp].second.pos + genome.header.pos[chromIndex] << "\t"
<< 1 << endl;
}
}
else {
if (inv_str == 0) {
pSclust << (*BtwnPairs)[bp].first.pos << "\t"
<< (*BtwnPairs)[bp].second.pos + genome.header.pos[chromIndex] << "\t"
<< (*BtwnPairs)[bp].first.pos + tinyOpts.globalK << "\t"
<< (*BtwnPairs)[bp].second.pos + tinyOpts.globalK + genome.header.pos[chromIndex]<< "\t"
<< 0 << endl;
}
else if (inv_str == 1) {
pSclust << read.length - (*BtwnPairs)[bp].first.pos - tinyOpts.globalK << "\t"
<< (*BtwnPairs)[bp].second.pos + tinyOpts.globalK + genome.header.pos[chromIndex] << "\t"
<< read.length - (*BtwnPairs)[bp].first.pos << "\t"
<< (*BtwnPairs)[bp].second.pos + genome.header.pos[chromIndex] << "\t"
<< 1 << endl;
}
}
}
pSclust.close();
ofstream eSclust("ExtendBtwnPairs.tab", std::ofstream::app);
for (int bp = ExtendBtwnPairs.size()-1; bp >= 0; bp--) {
if (inversion == 0) {
if (str == 0) {
eSclust << ExtendBtwnPairs[bp].first.pos << "\t"
<< ExtendBtwnPairs[bp].second.pos + genome.header.pos[chromIndex]<< "\t"
<< ExtendBtwnPairs[bp].first.pos + ExtendBtwnPairsMatchesLength[bp] << "\t"
<< ExtendBtwnPairs[bp].second.pos + ExtendBtwnPairsMatchesLength[bp] + genome.header.pos[chromIndex]<< "\t"
<< 0 << endl;
}
else if (str == 1) {
eSclust << read.length - ExtendBtwnPairs[bp].first.pos - ExtendBtwnPairsMatchesLength[bp] << "\t"
<< ExtendBtwnPairs[bp].second.pos + ExtendBtwnPairsMatchesLength[bp] + genome.header.pos[chromIndex] << "\t"
<< read.length - ExtendBtwnPairs[bp].first.pos << "\t"
<< ExtendBtwnPairs[bp].second.pos + genome.header.pos[chromIndex] << "\t"
<< 1 << endl;
}
}
else {
if (inv_str == 0) {
eSclust << ExtendBtwnPairs[bp].first.pos << "\t"
<< ExtendBtwnPairs[bp].second.pos + genome.header.pos[chromIndex] << "\t"
<< ExtendBtwnPairs[bp].first.pos + ExtendBtwnPairsMatchesLength[bp] << "\t"
<< ExtendBtwnPairs[bp].second.pos + ExtendBtwnPairsMatchesLength[bp] + genome.header.pos[chromIndex] << "\t"
<< 0 << endl;
}
else if (inv_str == 1) {
eSclust << read.length - ExtendBtwnPairs[bp].first.pos - ExtendBtwnPairsMatchesLength[bp] << "\t"
<< ExtendBtwnPairs[bp].second.pos + ExtendBtwnPairsMatchesLength[bp] + genome.header.pos[chromIndex] << "\t"
<< read.length - ExtendBtwnPairs[bp].first.pos << "\t"
<< ExtendBtwnPairs[bp].second.pos + genome.header.pos[chromIndex]<< "\t"
<< 1 << endl;
}
}
}
eSclust.close();
}
if (tinyOpts.dotPlot and tinyOpts.readname == read.name) {
ofstream Sclust("SparseDP_Forward.tab", std::ofstream::app);
for (int btc = BtwnChain.size()-1; btc >= 0; btc--) {
if (inversion == 0) {
if (str == 0) {
Sclust << ExtendBtwnPairs[BtwnChain[btc]].first.pos << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + genome.header.pos[chromIndex]<< "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].first.pos + ExtendBtwnPairsMatchesLength[BtwnChain[btc]] << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + ExtendBtwnPairsMatchesLength[BtwnChain[btc]] + genome.header.pos[chromIndex]<< "\t"
<< 0 << endl;
}
else if (str == 1) {
Sclust << read.length - ExtendBtwnPairs[BtwnChain[btc]].first.pos - ExtendBtwnPairsMatchesLength[BtwnChain[btc]] << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + ExtendBtwnPairsMatchesLength[BtwnChain[btc]] + genome.header.pos[chromIndex]<< "\t"
<< read.length - ExtendBtwnPairs[BtwnChain[btc]].first.pos << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + genome.header.pos[chromIndex]<< "\t"
<< 1 << endl;
}
}
else {
if (inv_str == 0) {
Sclust << ExtendBtwnPairs[BtwnChain[btc]].first.pos << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + genome.header.pos[chromIndex] << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].first.pos + ExtendBtwnPairsMatchesLength[BtwnChain[btc]] << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + ExtendBtwnPairsMatchesLength[BtwnChain[btc]] + genome.header.pos[chromIndex]<< "\t"
<< 0 << endl;
}
else if (inv_str == 1) {
Sclust << read.length - ExtendBtwnPairs[BtwnChain[btc]].first.pos - ExtendBtwnPairsMatchesLength[BtwnChain[btc]] << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + ExtendBtwnPairsMatchesLength[BtwnChain[btc]] + genome.header.pos[chromIndex] << "\t"
<< read.length - ExtendBtwnPairs[BtwnChain[btc]].first.pos << "\t"
<< ExtendBtwnPairs[BtwnChain[btc]].second.pos + genome.header.pos[chromIndex] << "\t"
<< 1 << endl;
}
}
}
Sclust.close();
}
//
// Use linear alignment to ligand the gap between local SDP chain;
//
GenomePos btc_curReadEnd, btc_nextReadStart, btc_curGenomeEnd, btc_nextGenomeStart;
btc_curReadEnd = curReadEnd;
btc_curGenomeEnd = curGenomeEnd;
int btc_end = BtwnChain.size()-1; int btc_start = 0;
if (BtwnChain.back() == ExtendBtwnPairs.size()-1) btc_end = BtwnChain.size()-2;
if (BtwnChain[0] == ExtendBtwnPairs.size()-2) btc_start = 1;
if (inversion == 1) {
alignment->UpdateParameters(str, tinyOpts, LookUpTable, svsigstrm, strands);
Alignment *inv_alignment = new Alignment(inv_value, strands[str], read.seq, read.length, read.name, inv_str, read.qual, genome.seqs[chromIndex],
genome.lengths[chromIndex], genome.header.names[chromIndex], chromIndex);
inv_alignment->NumOfAnchors1 = BtwnChain.size();
inv_alignment->NumOfAnchors0 = BtwnChain.size();
inv_alignment->Supplymentary = 1;
alignments.back().SegAlignment.push_back(inv_alignment);
}
for (int btc = btc_end; btc >= btc_start; btc--) {
btc_nextGenomeStart = ExtendBtwnPairs[BtwnChain[btc]].second.pos;
btc_nextReadStart = ExtendBtwnPairs[BtwnChain[btc]].first.pos;
RefineByLinearAlignment(btc_curReadEnd, btc_curGenomeEnd, btc_nextReadStart, btc_nextGenomeStart, str, chromIndex,
alignments.back().SegAlignment.back(), read, genome, strands, scoreMat, pathMat, tinyOpts, buff);
alignments.back().SegAlignment.back()->blocks.push_back(Block(ExtendBtwnPairs[BtwnChain[btc]].first.pos, ExtendBtwnPairs[BtwnChain[btc]].second.pos,
ExtendBtwnPairsMatchesLength[BtwnChain[btc]]));
debug_alignment(alignments.back().SegAlignment.back(), read.length, genome.lengths[chromIndex]);
btc_curReadEnd = btc_nextReadStart + ExtendBtwnPairsMatchesLength[BtwnChain[btc]];
btc_curGenomeEnd = btc_nextGenomeStart + ExtendBtwnPairsMatchesLength[BtwnChain[btc]];
}
//
// Add the linear alignment after the last anchor on BtwnChain;
//
btc_nextGenomeStart = nextGenomeStart;
btc_nextReadStart = nextReadStart;
if (btc_nextGenomeStart > btc_curGenomeEnd and btc_nextReadStart > btc_curReadEnd) {
RefineByLinearAlignment(btc_curReadEnd, btc_curGenomeEnd, btc_nextReadStart, btc_nextGenomeStart, str, chromIndex,
alignments.back().SegAlignment.back(), read, genome, strands, scoreMat, pathMat, tinyOpts, buff);
}
}
else {
RefineByLinearAlignment(curReadEnd, curGenomeEnd, nextReadStart, nextGenomeStart, str, chromIndex,
alignment, read, genome, strands, scoreMat, pathMat, tinyOpts, buff);
}
}
else {
RefineByLinearAlignment(curReadEnd, curGenomeEnd, nextReadStart, nextGenomeStart, str, chromIndex,
alignment, read, genome, strands, scoreMat, pathMat, tinyOpts, buff);
}
}
// else genomeThres = curGenomeEnd;
return;
}
void
LocalRefineAlignment(vector<Primary_chain> &Primary_chains, vector<SplitChain> &splitchains, vector<Cluster_SameDiag *> &ExtendClusters,
vector<SegAlignmentGroup> &alignments, Options smallOpts, const vector<float> & LookUpTable, Read &read, char *strands[2], int &p, int &h,
Genome &genome, int &LSC, const Options &tinyOpts, AffineAlignBuffers &buff, ostream *svsigstrm, vector<Cluster> &extend_clusters, bool refineEnd=true) {
for (int st = 0; st < splitchains.size(); st++) {
//
// Apply SparseDP on extended anchors on every splitchain;
// INPUT: vector<unsigned int> splitchain, vector<Cluster> ExtendClusters; OUTPUT: FinalChain finalchain;
//
FinalChain finalchain(&ExtendClusters);
smallOpts.freeGap=5;
SparseDP(splitchains[st], ExtendClusters, finalchain, smallOpts, LookUpTable, read);
//timing.Tick("2nd SDP");
if (tinyOpts.RemovePairedIndels) {
RemoveSmallPairedIndels<FinalChain> (finalchain);
RemovePairedIndels<FinalChain>(finalchain, refineEnd);
}
if (tinyOpts.RemoveSpuriousAnchors) RemoveSpuriousAnchors(finalchain);
//
// switch back to the original anchors;
//
UltimateChain ultimatechain;
SwitchToOriginalAnchors(finalchain, ultimatechain, ExtendClusters, extend_clusters);
finalchain.clear();
//cerr << "2nd SDP done!" << endl;
if (ultimatechain.size() == 0) continue; // cannot be mapped to the genome!
//
// Refine and store the alignment; NOTICE: when filling in the space between two adjacent anchors,
// the process works in forward direction, so we need to flip the small matches
// found in the spaces before insert them into the alignment if necessary;
// INPUT: vector<int> finalchainSeperateStrand; OUTPUT: Alignment *alignment;
//
int ad = alignments.back().SegAlignment.size();
int start = 0, end = ultimatechain.size();
assert(start < end);
bool str = ultimatechain.strand(start);
int cln = ultimatechain.ClusterNum(start);
int chromIndex = extend_clusters[cln].chromIndex;
/*
// DELETE LATER
for (int ep = 0; ep < ultimatechain.size(); ep++) {
cerr << ultimatechain[ep].second.pos << "\t" << genome.lengths[chromIndex] << endl;
assert(ultimatechain[ep].second.pos < genome.lengths[chromIndex]);
}
*/
if (smallOpts.dotPlot and read.name == smallOpts.readname ) {
ofstream clust("SparseDP.tab", ofstream::app);
for (int ep = 0; ep < ultimatechain.size(); ep++) {
if (ultimatechain.strand(ep) == 0) {
clust << ultimatechain[ep].first.pos << "\t"
<< ultimatechain[ep].second.pos + genome.header.pos[chromIndex] << "\t"
<< ultimatechain[ep].first.pos + ultimatechain.length(ep) << "\t"
<< ultimatechain[ep].second.pos + ultimatechain.length(ep) + genome.header.pos[chromIndex]<< "\t"
<< st << "\t"
<< ultimatechain.ClusterNum(ep) << "\t"
<< ultimatechain.strand(ep) << endl;
}
else {
clust << ultimatechain[ep].first.pos << "\t"
<< ultimatechain[ep].second.pos + ultimatechain.length(ep) + genome.header.pos[chromIndex]<< "\t"
<< ultimatechain[ep].first.pos + ultimatechain.length(ep) << "\t"
<< ultimatechain[ep].second.pos + genome.header.pos[chromIndex] << "\t"
<< st << "\t"
<< ultimatechain.ClusterNum(ep) << "\t"
<< ultimatechain.strand(ep) << endl;
}
}
clust.close();
}
Alignment *alignment = new Alignment(Primary_chains[p].chains[h].value, strands[str], read.seq, read.length,
read.name, str, read.qual, genome.seqs[chromIndex], genome.lengths[chromIndex],
genome.header.names[chromIndex], chromIndex);
alignment->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
alignment->NumOfAnchors1 = end - start;
alignment->SecondSDPValue = ultimatechain.SecondSDPValue;
alignments.back().SegAlignment.push_back(alignment);
vector<int> scoreMat;
vector<Arrow> pathMat;
//
// Set the secondary or supplymentary flag for the alignment;
//
if (h > 0) alignment->ISsecondary = 1;
if (st != LSC) alignment->Supplymentary = 1;
bool inv_str = 0, inversion = 0, breakalignment = 0, prev_inv = 0;
if (str == 0) {
int last = end - 1;
int fl = end - 1;
inv_str = 1; prev_inv = end - 1;
while (fl > start) {
int cur = fl;
int next = fl - 1;
//
// Check the distance between two anchors. If the distance is too large, refine anchors and apply 3rd SDP;
// Otherwise apply linear alignment.
//
RefinedAlignmentbtwnAnchors(cur, next, str, inv_str, chromIndex, ultimatechain, alignments, alignments.back().SegAlignment.back(),
read, genome, strands, scoreMat, pathMat, tinyOpts, buff,
LookUpTable, inversion, breakalignment, svsigstrm);
//DELETE LATER
for (int bi=0; bi < alignments.back().SegAlignment.back()->blocks.size(); bi++) {
assert(alignments.back().SegAlignment.back()->blocks[bi].tPos < genome.lengths[chromIndex]);
}
if (inversion == 1 or breakalignment == 1) { // an inversion found in between two anchors; Need to make a new alignment for the next
// alignments.back().SegAlignment.back()->UpdateParameters(inv_str, smallOpts, LookUpTable, svsigstrm, strands);
if (inversion == 1) alignments.back().SegAlignment.back()->UpdateParameters(inv_str, smallOpts, LookUpTable, svsigstrm, strands);
else alignments.back().SegAlignment.back()->UpdateParameters(str, smallOpts, LookUpTable, svsigstrm, strands);
alignments.back().SegAlignment.back()->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = last - fl;
Alignment *next_alignment = new Alignment(Primary_chains[p].chains[h].value, strands[str], read.seq, read.length,
read.name, str, read.qual, genome.seqs[chromIndex], genome.lengths[chromIndex],
genome.header.names[chromIndex], chromIndex);
// next_alignment->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
// next_alignment->NumOfAnchors1 = fl - start;
next_alignment->Supplymentary = 1;
alignments.back().SegAlignment.push_back(next_alignment);
last = fl;
prev_inv = fl;
inversion = 0;
breakalignment = 0;
}
fl--;
}
alignments.back().SegAlignment.back()->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = last - fl;
assert(ultimatechain[start].second.pos < genome.lengths[chromIndex]);
alignments.back().SegAlignment.back()->blocks.push_back(Block(ultimatechain[start].first.pos, ultimatechain[start].second.pos,
ultimatechain.length(start)));
}
else {
int last = start;
int fl = start;
inv_str = 0; prev_inv = start;
while (fl < end - 1) {
int cur = fl;
int next = fl + 1;
RefinedAlignmentbtwnAnchors(cur, next, str, inv_str, chromIndex, ultimatechain, alignments, alignments.back().SegAlignment.back(),
read, genome, strands, scoreMat, pathMat, tinyOpts, buff,
LookUpTable, inversion, breakalignment, svsigstrm);
//DELETE LATER
for (int bi=0; bi < alignments.back().SegAlignment.back()->blocks.size(); bi++) {
assert(alignments.back().SegAlignment.back()->blocks[bi].tPos < genome.lengths[chromIndex]);
}
if (inversion == 1 or breakalignment == 1) {
if (inversion == 1) alignments.back().SegAlignment.back()->UpdateParameters(inv_str, smallOpts, LookUpTable, svsigstrm, strands);
else alignments.back().SegAlignment.back()->UpdateParameters(str, smallOpts, LookUpTable, svsigstrm, strands);
// alignments.back().SegAlignment.back()->UpdateParameters(inv_str, smallOpts, LookUpTable, svsigstrm, strands);
alignments.back().SegAlignment.back()->NumOfAnchors1 = fl - last;
alignments.back().SegAlignment.back()->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
Alignment *next_alignment = new Alignment(Primary_chains[p].chains[h].value, strands[str], read.seq, read.length,
read.name, str, read.qual, genome.seqs[chromIndex], genome.lengths[chromIndex],
genome.header.names[chromIndex], chromIndex);
// next_alignment->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
// next_alignment->NumOfAnchors1 = end-fl;
next_alignment->Supplymentary = 1;
alignments.back().SegAlignment.push_back(next_alignment);
last = fl;
prev_inv = fl;
inversion = 0;
breakalignment = 0;
}
fl++;
}
alignments.back().SegAlignment.back()->NumOfAnchors0 = Primary_chains[p].chains[h].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = fl - last;
assert(ultimatechain[end-1].second.pos < genome.lengths[chromIndex]);
alignments.back().SegAlignment.back()->blocks.push_back(Block(read.length - ultimatechain[end - 1].first.pos - ultimatechain.length(end - 1),
ultimatechain[end - 1].second.pos, ultimatechain.length(end - 1)));
}
// // debug checking
// for (int bb = 1; bb < alignments.back().SegAlignment.back()->blocks.size(); bb++) {
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].qPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= read.length);
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].tPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= genome.lengths[chromIndex]);
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].qPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= alignments.back().SegAlignment.back()->blocks[bb].qPos);
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].tPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= alignments.back().SegAlignment.back()->blocks[bb].tPos);
// }
//
// Set some parameters in Alignment alignment
//
alignments.back().SegAlignment.back()->UpdateParameters(str, smallOpts, LookUpTable, svsigstrm, strands);
ultimatechain.clear();
//
// Decide the inversion flag for each segment alignment (PAF format); seek +,-,+ or -,+,-
//
int js = ad + 2;
while (js < alignments.back().SegAlignment.size()) {
if ((alignments.back().SegAlignment[js-2]->strand == 0 and alignments.back().SegAlignment[js-1]->strand == 1
and alignments.back().SegAlignment[js]->strand == 0) or ((alignments.back().SegAlignment[js-2]->strand == 1
and alignments.back().SegAlignment[js-1]->strand == 0 and alignments.back().SegAlignment[js]->strand == 1))) {
//
// inversion cannot be too far (<10,000) from alignments at both sides;
//
if (alignments.back().SegAlignment[js-1]->tStart > alignments.back().SegAlignment[js-2]->tEnd + 10000
or alignments.back().SegAlignment[js]->tStart > alignments.back().SegAlignment[js-1]->tEnd + 10000) {
js++;
continue;
}
//
// length requirements;
//
else if (alignments.back().SegAlignment[js]->nm < 500 or alignments.back().SegAlignment[js-1]->nm < 500
or alignments.back().SegAlignment[js-2]->nm < 40 or alignments.back().SegAlignment[js-2]->nm > 15000) {
js++;
continue;
}
else if (alignments.back().SegAlignment[js-2]->typeofaln != 3) {
alignments.back().SegAlignment[js-1]->typeofaln=3;
}
}
js++;
}
}
}
// void RefindEnds(GenomePos &qPos, int cur, UltimateChain &chain, bool str, Alignment *alignment, const Options &opts,
// Genome &genome, Read &read, int &chromIndex, char *strands[2], vector<int> &scoreMat,
// vector<Arrow> &pathMat, AffineAlignBuffers &buff, const vector<float> & LookUpTable, bool block = 1) { // block = 1: right, block = 0: left
// GenomePos curGenomeEnd, curReadEnd, nextGenomeStart, nextReadStart;
// if (block) { // right
// if (qPos <= chain.qEnd(cur) + 100) return;
// if (str == 0) { // forward
// curReadEnd = chain.qEnd(cur); nextReadStart = qPos - 100;
// curGenomeEnd = chain.tEnd(cur); nextGenomeStart = curGenomeEnd + (nextReadStart - curReadEnd);
// }
// else { // flip the space if it is reversed stranded
// curReadEnd = read.length - (qPos - 100); nextReadStart = read.length - chain.qEnd(cur);
// nextGenomeStart = chain.tStart(cur); curGenomeEnd = nextGenomeStart - (nextReadStart - curReadEnd);
// }
// }
// else { // left
// if (chain.qStart(cur) <= qPos + 100) return;
// if (str == 0) {
// curReadEnd = qPos + 100; nextReadStart = chain.qStart(cur);
// curGenomeEnd = chain.tStart(cur) - (nextReadStart - curReadEnd); nextGenomeStart = chain.tStart(cur);
// }
// else {
// curReadEnd = read.length - chain.qStart(cur); nextReadStart = read.length - (qPos + 100);
// curGenomeEnd = chain.tStart(cur) - (nextReadStart - curReadEnd); nextGenomeStart = chain.tStart(cur);
// }
// }
// assert(curGenomeEnd <= nextGenomeStart);
// assert(curReadEnd <= nextReadStart);
// if (curGenomeEnd >= nextGenomeStart + 100 or curReadEnd >= nextReadStart + 100) return;
// GenomePairs EndPairs;
// RefineSpace(opts.globalK, opts.globalW, 20, 0, EndPairs, opts, genome, read, strands, chromIndex, nextReadStart, curReadEnd, nextGenomeStart, curGenomeEnd, str);
// if (EndPairs.size() > 0 and (EndPairs.size() / (float) (nextReadStart - curReadEnd)) >= opts.anchorstoosparse ) {
// GenomePairs ExtendEndPairs; vector<int> ExtendEndPairsMatchesLength; vector<unsigned int> EndChain;
// LinearExtend(&EndPairs, ExtendEndPairs, ExtendEndPairsMatchesLength, opts, genome, read, chromIndex, 0, 0, opts.globalK);
// TrimOverlappedAnchors(ExtendEndPairs, ExtendEndPairsMatchesLength);
// float value = 0; int NumofAnchors = 0;
// SparseDP_ForwardOnly(ExtendEndPairs, ExtendEndPairsMatchesLength, EndChain, opts, LookUpTable, value, NumofAnchors, 1/2); //1
// RemovePairedIndels(ExtendEndPairs, EndChain, ExtendEndPairsMatchesLength);
// if (opts.dotPlot and !opts.readname.empty() and read.name == opts.readname) {
// ofstream eSclust("ExtendBtwnPairs.tab", std::ofstream::app);
// for (int bp = ExtendEndPairs.size()-1; bp >= 0; bp--) {
// if (str == 0) {
// eSclust << ExtendEndPairs[bp].first.pos << "\t"
// << ExtendEndPairs[bp].second.pos << "\t"
// << ExtendEndPairs[bp].first.pos + ExtendEndPairsMatchesLength[bp] << "\t"
// << ExtendEndPairs[bp].second.pos + ExtendEndPairsMatchesLength[bp] << "\t"
// << 0 << endl;
// }
// else if (str == 1) {
// eSclust << read.length - ExtendEndPairs[bp].first.pos - ExtendEndPairsMatchesLength[bp] << "\t"
// << ExtendEndPairs[bp].second.pos + ExtendEndPairsMatchesLength[bp] << "\t"
// << read.length - ExtendEndPairs[bp].first.pos << "\t"
// << ExtendEndPairs[bp].second.pos << "\t"
// << 1 << endl;
// }
// }
// eSclust.close();
// if (opts.dotPlot and read.name == opts.readname) {
// ofstream Sclust("SparseDP_Forward.tab", std::ofstream::app);
// for (int btc = EndChain.size()-1; btc >= 0; btc--) {
// if (str == 0) {
// Sclust << ExtendEndPairs[EndChain[btc]].first.pos << "\t"
// << ExtendEndPairs[EndChain[btc]].second.pos << "\t"
// << ExtendEndPairs[EndChain[btc]].first.pos + ExtendEndPairsMatchesLength[EndChain[btc]] << "\t"
// << ExtendEndPairs[EndChain[btc]].second.pos + ExtendEndPairsMatchesLength[EndChain[btc]] << "\t"
// << 0 << endl;
// }
// else if (str == 1) {
// Sclust << read.length - ExtendEndPairs[EndChain[btc]].first.pos - ExtendEndPairsMatchesLength[EndChain[btc]] << "\t"
// << ExtendEndPairs[EndChain[btc]].second.pos + ExtendEndPairsMatchesLength[EndChain[btc]] << "\t"
// << read.length - ExtendEndPairs[EndChain[btc]].first.pos << "\t"
// << ExtendEndPairs[EndChain[btc]].second.pos << "\t"
// << 1 << endl;
// }
// }
// Sclust.close();
// }
// }
// //
// // Use linear alignment to ligand the gap between local SDP chain;
// //
// GenomePos btc_curReadEnd, btc_nextReadStart, btc_curGenomeEnd, btc_nextGenomeStart;
// btc_curReadEnd = curReadEnd; btc_curGenomeEnd = curGenomeEnd;
// for (int btc = EndChain.size() - 1; btc >= 0; btc--) {
// btc_nextGenomeStart = ExtendEndPairs[EndChain[btc]].second.pos;
// btc_nextReadStart = ExtendEndPairs[EndChain[btc]].first.pos;
// RefineByLinearAlignment(btc_curReadEnd, btc_curGenomeEnd, btc_nextReadStart, btc_nextGenomeStart, str, chromIndex, alignment, read, genome, strands, scoreMat, pathMat, opts, buff);
// alignment->blocks.push_back(Block(ExtendEndPairs[EndChain[btc]].first.pos, ExtendEndPairs[EndChain[btc]].second.pos, ExtendEndPairsMatchesLength[EndChain[btc]]));
// debug_alignment(alignment, read.length, genome.lengths[chromIndex]);
// btc_curReadEnd = btc_nextReadStart + ExtendEndPairsMatchesLength[EndChain[btc]];
// btc_curGenomeEnd = btc_nextGenomeStart + ExtendEndPairsMatchesLength[EndChain[btc]];
// }
// //
// // Add the linear alignment after the last anchor on BtwnChain;
// //
// if (block == 0) {
// btc_nextGenomeStart = nextGenomeStart;
// btc_nextReadStart = nextReadStart;
// if (btc_nextGenomeStart > btc_curGenomeEnd and btc_nextReadStart > btc_curReadEnd) {
// RefineByLinearAlignment(btc_curReadEnd, btc_curGenomeEnd, btc_nextReadStart, btc_nextGenomeStart, str, chromIndex,
// alignment, read, genome, strands, scoreMat, pathMat, opts, buff);
// }
// }
// }
// else {return;}
// return;
// }
//
// For chaining of pure matches
//
void
LocalRefineAlignment( vector<UltimateChain> &ultimatechains, vector<Cluster> &ext_clusters, vector<SegAlignmentGroup> &alignments, const Options &smallOpts,
const vector<float> & LookUpTable, Read &read, char *strands[2], int &h, Genome &genome, int &LSC, const Options &tinyOpts, AffineAlignBuffers &buff, ostream *svsigstrm){
for (int st = 0; st < ultimatechains.size(); st++) {
if (ultimatechains[st].size() <= 1) continue;
// Refine and store the alignment; NOTICE: when filling in the space between two adjacent anchors,
// the process works in forward direction, so we need to flip the small matches
// found in the spaces before insert them into the alignment if necessary;
// INPUT: vector<int> finalchainSeperateStrand; OUTPUT: Alignment *alignment;
//
int ad = alignments.back().SegAlignment.size();
int start = 0, end = ultimatechains[st].size() - 1;
// assert(start < end);
bool str = ultimatechains[st].strand(start);
int cln = ultimatechains[st].ClusterNum(start);
int chromIndex = ext_clusters[cln].chromIndex;
Alignment *alignment = new Alignment(ultimatechains[st].FirstSDPValue, strands[str], read.seq, read.length,
read.name, str, read.qual, genome.seqs[chromIndex], genome.lengths[chromIndex],
genome.header.names[chromIndex], chromIndex);
alignment->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
alignment->NumOfAnchors1 = ultimatechains[st].NumOfAnchors1;
alignments.back().SegAlignment.push_back(alignment);
vector<int> scoreMat;
vector<Arrow> pathMat;
//
// Set the secondary or supplymentary flag for the alignment;
//
if (h > 0) alignment->ISsecondary = 1;
if (st != LSC) alignment->Supplymentary = 1;
GenomePos qPos = 0;
bool inv_str = 0, inversion = 0, breakalignment = 0, prev_inv = 0;
if (str == 0) {
int last = end;
int fl = end; inv_str = 1; prev_inv = end;
while (fl > start) {
int cur = fl;
int next = fl - 1;
//
// Check the distance between two anchors. If the distance is too large, refine anchors and apply 3rd SDP;
// Otherwise apply linear alignment.
//
RefinedAlignmentbtwnAnchors(cur, next, str, inv_str, chromIndex, ultimatechains[st], alignments, alignments.back().SegAlignment.back(),
read, genome, strands, scoreMat, pathMat, tinyOpts, buff,
LookUpTable, inversion, breakalignment, svsigstrm);
if (inversion == 1 or breakalignment == 1) { // an inversion found in between two anchors
if (inversion == 1) alignments.back().SegAlignment.back()->UpdateParameters(inv_str, smallOpts, LookUpTable, svsigstrm, strands);
else alignments.back().SegAlignment.back()->UpdateParameters(str, smallOpts, LookUpTable, svsigstrm, strands);
alignments.back().SegAlignment.back()->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = last - fl;
Alignment *next_alignment = new Alignment(ultimatechains[st].FirstSDPValue, strands[str], read.seq, read.length,
read.name, str, read.qual, genome.seqs[chromIndex], genome.lengths[chromIndex],
genome.header.names[chromIndex], chromIndex);
next_alignment->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
// alignments.back().SegAlignment.back()->NumOfAnchors1 = last - fl;
last = fl;
next_alignment->Supplymentary = 1;
alignments.back().SegAlignment.push_back(next_alignment);
prev_inv = fl;
inversion = 0;
breakalignment = 0;
}
fl--;
}
alignments.back().SegAlignment.back()->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = last - fl;
assert(ultimatechains[st][start].second.pos < genome.lengths[chromIndex]);
alignments.back().SegAlignment.back()->blocks.push_back(Block(ultimatechains[st][start].first.pos, ultimatechains[st][start].second.pos, ultimatechains[st].length(start)));
}
else {
int last = start;
int fl = start;
inv_str = 0; prev_inv = start;
while (fl < end) {
int cur = fl;
int next = fl + 1;
RefinedAlignmentbtwnAnchors(cur, next, str, inv_str, chromIndex, ultimatechains[st], alignments, alignments.back().SegAlignment.back(),
read, genome, strands, scoreMat, pathMat, tinyOpts, buff,
LookUpTable, inversion, breakalignment, svsigstrm);
if (inversion == 1 or breakalignment == 1) {
if (inversion == 1) alignments.back().SegAlignment.back()->UpdateParameters(inv_str, smallOpts, LookUpTable, svsigstrm, strands);
else alignments.back().SegAlignment.back()->UpdateParameters(str, smallOpts, LookUpTable, svsigstrm, strands);
alignments.back().SegAlignment.back()->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = fl - last;
Alignment *next_alignment = new Alignment(ultimatechains[st].FirstSDPValue, strands[str], read.seq, read.length,
read.name, str, read.qual, genome.seqs[chromIndex], genome.lengths[chromIndex],
genome.header.names[chromIndex], chromIndex);
next_alignment->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
last = fl;
next_alignment->Supplymentary = 1;
alignments.back().SegAlignment.push_back(next_alignment);
prev_inv = fl;
inversion = 0;
breakalignment = 0;
}
fl++;
}
alignments.back().SegAlignment.back()->NumOfAnchors0 = ultimatechains[st].NumOfAnchors0;
alignments.back().SegAlignment.back()->NumOfAnchors1 = fl - last;
assert(ultimatechains[st][start].second.pos < genome.lengths[chromIndex]);
alignments.back().SegAlignment.back()->blocks.push_back(Block(read.length - ultimatechains[st][end].first.pos - ultimatechains[st].length(end), ultimatechains[st][end].second.pos, ultimatechains[st].length(end)));
}
// // debug checking
// for (int bb = 1; bb < alignments.back().SegAlignment.back()->blocks.size(); bb++) {
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].qPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= read.length);
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].tPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= genome.lengths[chromIndex]);
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].qPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= alignments.back().SegAlignment.back()->blocks[bb].qPos);
// assert(alignments.back().SegAlignment.back()->blocks[bb-1].tPos + alignments.back().SegAlignment.back()->blocks[bb-1].length <= alignments.back().SegAlignment.back()->blocks[bb].tPos);
// }
//
// Set some parameters in Alignment alignment
//
alignments.back().SegAlignment.back()->UpdateParameters(str, smallOpts, LookUpTable, svsigstrm, strands);
//
// Decide the inversion flag for each segment alignment (PAF format); seek +,-,+ or -,+,-
//
int js = ad + 2;