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main.cpp
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/**
* @file main.cpp
* @author Amirhosein Afshinfard <afshinfard(at)ce(.)sharif(.)edu>
* <afshinfard(at)gmail(.)com>
* Bioinformatics Technology Lab - GSC @ BC Cancer Agency
* University of British Columbia
* Bioinformatics Research Lab - Sharif Uiversity of Technology
*
* @cite
*
* @copyright (c) 2017
*
* Amirhosein Afshinfard <afshinfard(at)ce (.)sharif(.)edu>
* <afshinfard(at)gmail(.)com>
* Damoon Nashta-ali <damoun_dna(at)yahoo(.)com>
* Seyed Abolfazl Motahari <motahari(at)sharif(.)edu>
*
**/
#include "Header.h"
#include "ExtraTools.h"
#include "WriteResults.h"
#include "DataStructures.h"
//#include "SureMap.h"
#include "LocalAligner.h"
// ================================|
//> Global Vars: |
// ================================|
// |
//> Binary Genomes
vector<bool> bGRight;
vector<bool> bGLeft;
vector<informativeChunk> informativeChunks;
vector<feasibleEvents> rightE;
vector<feasibleEvents> leftE;
//double mappingTime = 0;
//double extensionTime = 0;
clock_t mappingTime = 0;
clock_t extensionTime = 0;
long long connectedCntr = 0;
long long totalReads = 0;
long long readCounter = 0;
long long genomeLength = 0;
readMappingInfo globalRMI[MAXTHREADS];
int shiftSteps = chunkSize / shiftIterations ;
// |
// ================================'
// ================================|
//> Functions: |
// ================================|
// |
// ================================|
// Detection part |
// Detection part |
// ================================'
inline void changeBinGenome(long long start , long long end, bool isToRight){
if(start > end){
long long temp = start;
start = end;
end = temp;
}
//BGRchanges += abs(end - start)+1;
if( isToRight ){
bGRChangeMutex.lock();
for(long long i = start; i < end+1 ; i++)
bGRight[i] = true;
bGRChangeMutex.unlock();
}else{
bGLChangeMutex.lock();
for(long long i = start; i < end+1 ; i++)
bGLeft[i] = true;
bGLChangeMutex.unlock();
}
}
inline mapResult uniqueMap( string readChunk , string quality, int idx ){
// [Completed]
// Func aim:
// given a read chunk, it's quality an thread index
// return the unique mapping result for this chunk
//time_t timer = time(NULL);
clock_t timer = clock();
globalRMI[idx].read = readChunk;
globalRMI[idx].qual = quality;
// globalRMI[idx].readName = "?";
vector< mappingInfo > mps = getAllMapping( idx, globalRMI[idx] );
string mos = readChunk;
string rev = reverseComplement( readChunk );
// if( mps.size() > 1 ){
// cerr<<"not a unique search";
// mappingTime += clock() - timer;
// return mapResult();
// }
mappingInfo ix = mps[0];
if( ix.flag != 4 ){
ix.cigar = getCigar( ix.refPos, ( ix.flag == 0 ) ? mos : rev, ix.acceptedValue, idx );
ix.refPos = ix.refPos - ix.acceptedValue + ix.cigar.second;
}else{
mappingTime += clock() - timer;
return mapResult( -1 , false );
}
mappingTime += clock() - timer;
return mapResult(ix.refPos,( ix.flag == 0 ? false : true ));
}
inline int ifAlignable( long long startLoci, string readSegment, bool isReverse, int *alignShiftPos
/*,bool isToRight, jumpsCount, (counter==0 && onlyBG ? true:false)*/ ){
if( isReverse )
readSegment = revComplemACGT( readSegment );
double indelShiftLocal = indelShift /*+ (numGap*jumpsCount)/chunkSize*/;
// bool binGenome;
// if( useBinGenome ){
// binGenome = checkBinGenome(startLoci, startLoci + this->chunkSize, false, (BGLR ? isToRight : true));
// if(binGenome){
// cntBG++;
// return 1;
// }
// if( onlyBGlocal )
// return 0;
// }
cntCOM++;
if(startLoci - indelShiftLocal*readSegment.size() < 0 || startLoci + indelShiftLocal*readSegment.size()+chunkSize > genomeLength-1 )
return 0;
//string genomeString = getGenomeHDD(startLoci - indelShiftLocal*readSegment.size(), chunkSize + 2*readSegment.size()*indelShiftLocal );
string genomeString = getGenome(startLoci - indelShiftLocal*readSegment.size(), chunkSize + 2*readSegment.size()*indelShiftLocal );
int readlen = readSegment.size();
string seqConstantB = "";
for(int i=0;i < (int)(indelShiftLocal*readlen);i++)
seqConstantB += "A";
readSegment += seqConstantB;
LocalAligner *local;
local = new LocalAligner(readSegment, genomeString, gapPen, misPen, matchPen, (int)(indelShiftLocal*readlen), (int)(editDistance*readlen) );
local->process();
local->backtrack();
//cout//<<local->realCigar << endl;
//cout<<local->cigar << endl;
int score = local->mScore;
char isAlignable = (score > localAlThreshold ? 2 : 0 );
if( isAlignable ){
*alignShiftPos = local->totalGapr - local->totalGapfa;
//previous shift if needed.
}
delete local;
return isAlignable;
}
long extendManager(long from, long until, string* read, solvedFragInfo* anchorExtendResult){
// [Completed] FUNC aim:
// to extend from from's neighbour (not from from itself) to until
// from < until not guaranteed! based on diretion it is feasible and returns number of lastly extended chunks
if(from == until)
return from;
long long startLoci = (from > until ? anchorExtendResult->startPos : anchorExtendResult->endPos);
int direction = (from > until ? -1 : +1);
bool isReverse = anchorExtendResult->isReverse;
// ====================================
// frags of read from from's neighour until until:
vector<string> fragsOfRead;
if(direction == 1){
for( int i = from; i < (until-1) ; i++ )
fragsOfRead.push_back( read->substr( (i*chunkSize) , chunkSize ));
if( until == (long) ((read->size() + chunkSize - 20) / chunkSize) )
fragsOfRead.push_back( read->substr( (until-1)*chunkSize /*, readLen-((readLen-1)/chunkSize)*chunkSize)*/ ));
else
fragsOfRead.push_back( read->substr( (until-1)*chunkSize , chunkSize ));
}else
for( int i = from-1; i >= until ; i-- )
fragsOfRead.push_back( read->substr( ((i-1)*chunkSize) , chunkSize ));
// ===============================================
// let's extend from from until until if possible:
int counter = 0;
int alignShiftPos = 0;
int successFlag = 0;
do{
startLoci += (direction*(chunkSize + alignShiftPos))*( isReverse ? -1 : 1 );
successFlag = ifAlignable( startLoci, fragsOfRead.at( counter ), isReverse, &alignShiftPos
/*,isToRight, jumpsCount, (counter==0 && onlyBG ? true:false)*/ );
counter += ( successFlag ? 1:0 );
//jumpsCount += ( successFlag == 1 ? 1:0);
}while( successFlag && counter < abs(from - until) );
// ========================
// data changes and return:
if(from > until){
if(BGChanges){
changeBinGenome(anchorExtendResult->startPos + (isReverse ? 0 : 2*chunkSize ),
anchorExtendResult->startPos-(isReverse?-1:+1)*(counter*chunkSize+alignShiftPos) + (isReverse ? -2 : 0 )*chunkSize,
true);
changeBinGenome(anchorExtendResult->startPos + (isReverse ? -1 : +1 )*chunkSize,
anchorExtendResult->startPos-(isReverse?-1:+1)*(counter*chunkSize+alignShiftPos) + ( -1 )*chunkSize,
false);
}
anchorExtendResult->startChunk = from - counter;
anchorExtendResult->startPos -= (isReverse?-1:+1)*(counter*chunkSize+alignShiftPos);
return anchorExtendResult->startChunk;
}else{
if(BGChanges){
changeBinGenome(anchorExtendResult->endPos + (isReverse ? 0 : 2*chunkSize ),
anchorExtendResult->endPos + (isReverse?-1:+1)*(counter*chunkSize+alignShiftPos) + (isReverse ? -2 : 0 )*chunkSize,
true);
changeBinGenome(anchorExtendResult->endPos + (isReverse ? -1 : +1 )*chunkSize,
anchorExtendResult->endPos + (isReverse?-1:+1)*(counter*chunkSize+alignShiftPos) + ( -1 )*chunkSize,
false);
}
anchorExtendResult->endChunk = from + counter;
anchorExtendResult->endPos += (isReverse?-1:+1)*(counter*chunkSize+alignShiftPos);
return anchorExtendResult->endChunk;
}
}
void allFragsExtension( string* read, vector<solvedFragInfo>* clusters, int idx ){
// time_t timer = time(NULL);
clock_t timer = clock();
mappingTime += clock() - timer;
int numFrags = ( read->size() + chunkSize - 20 ) / chunkSize;
sort( clusters->begin(), clusters->end() );
if( clusters->front().startChunk > 1 ){
extendManager( clusters->front().startChunk ,1 ,read ,&(clusters->front()) );
}
for( int i = 1 ; i < clusters->size() ; i++ ){
if(clusters->at(i-1).endChunk > clusters->at(i).startChunk){
cerr<<"\n baha'"<<endl;
continue;
}
extendManager( clusters->at(i-1).endChunk ,clusters->at(i).startChunk-1 ,read ,clusters->data()+i-1 );
extendManager( clusters->at(i).startChunk ,clusters->at(i-1).endChunk+1 ,read ,&(clusters->at(i)) );
}
if( clusters->back().endChunk < numFrags ){
extendManager( clusters->back().endChunk ,numFrags ,read ,&(clusters->back()) );
}
extensionTime += clock() - timer;
}
interval anchorAndExtend(string* read ,string* qc ,vector<interval>* checkStack ,int it
,array<vector<mapResult>, MAX_SHIFT_ITER>* mapResults
,vector<solvedFragInfo>* clusters
,int idx ){
// Remained: inExtend
// FUNC aim:
// Given [a single read], its [quality], its [incomplete mapping records] for different shifting
// and [asked Intervals] try to anchor and exend exactly for one cluster and push new intervals to checkStack
interval anchoredInterval;
//interval extendedInterval;
bool isAnchored = false;
solvedFragInfo anchorExtendResult;
interval toCheck = checkStack->back();
checkStack->pop_back();
bool isFinalChunk = ( ((long)(read->length() + chunkSize - 20) / chunkSize) == toCheck.end ? true : false );
// =====================
// Check First and Last:
if( mapResults->at(it)[toCheck.start-1].position == 0 )
mapResults->at(it)[toCheck.start-1] = uniqueMap( read->substr((toCheck.start-1)*chunkSize, chunkSize)
,qc->substr((toCheck.start-1)*chunkSize, chunkSize)
,idx );
if( mapResults->at(it)[toCheck.end-1].position == 0 )
mapResults->at(it)[toCheck.end-1] = uniqueMap( ( isFinalChunk ? read->substr((toCheck.end-1)*chunkSize)
: read->substr((toCheck.end-1)*chunkSize, chunkSize))
,( isFinalChunk ? qc->substr((toCheck.end-1)*chunkSize)
: qc->substr((toCheck.end-1)*chunkSize, chunkSize))
,idx );
if( mapResults->at(it)[toCheck.start-1].isReverse == mapResults->at(it)[toCheck.end-1].isReverse &&
abs(mapResults->at(it)[toCheck.start-1].position - mapResults->at(it)[toCheck.end-1].position
- pow(-1,(mapResults->at(it)[toCheck.start-1].isReverse == true ? 1:0 ))*(toCheck.start-toCheck.end)*chunkSize )
<
gapRate*abs(toCheck.start-toCheck.end) ){
// nothing to push to stack, this interval has been completely solved.
anchorExtendResult = solvedFragInfo(toCheck.start,mapResults->at(it)[toCheck.start-1].position,
toCheck.end, mapResults->at(it)[toCheck.end-1].position,
mapResults->at(it)[toCheck.start-1].isReverse, it * shiftSteps );
//clusters->push_back(anchorExtendResult);
//return toCheck;
anchoredInterval = toCheck;
isAnchored = true;
}
// =====================
// Check others:
int half = (long) ceil((double) (toCheck.end-toCheck.start)/2);
if( !isAnchored ){
// if ((toCheck.end-toCheck.start) %2 != 0) {
// half--;
// }
for (int i = 1; i < half; i++) {
// one from left with all rights
if( mapResults->at(it)[toCheck.start+i-1].position == 0 )
mapResults->at(it)[toCheck.start+i-1] = uniqueMap( read->substr((toCheck.start+i-1)*chunkSize, chunkSize)
,qc->substr((toCheck.start+i-1)*chunkSize, chunkSize)
,idx );
if( mapResults->at(it)[toCheck.start+i-1].position > 0 ){
for(int j = 0 ; j < i ; j++){
if( mapResults->at(it)[toCheck.start+i-1].isReverse == mapResults->at(it)[toCheck.end-j-1].isReverse &&
abs(mapResults->at(it)[toCheck.start+i-1].position - mapResults->at(it)[toCheck.end-j-1].position
- pow(-1,(mapResults->at(it)[toCheck.start+i-1].isReverse==true?1:0))*(toCheck.start+i-(toCheck.end-j))*chunkSize )
<
gapRate*abs(toCheck.start+i-toCheck.end-j) ){
anchoredInterval = interval( toCheck.start+i, toCheck.end-j);
isAnchored = true;
anchorExtendResult = solvedFragInfo(toCheck.start+i,mapResults->at(it)[toCheck.start+i-1].position,
toCheck.end-j, mapResults->at(it)[toCheck.end-j-1].position,
mapResults->at(it)[toCheck.start+i-1].isReverse, it * shiftSteps );
// add to readAnchorInfo DS
break;
}
}
}
if(isAnchored)
break;
// one from right with all lefts
if( mapResults->at(it)[toCheck.end-i-1].position == 0 )
mapResults->at(it)[toCheck.end-i-1] = uniqueMap( read->substr((toCheck.end-i-1)*chunkSize, chunkSize)
,qc->substr((toCheck.end-i-1)*chunkSize, chunkSize)
,idx );
if( mapResults->at(it)[toCheck.end-i-1].position > 0 ){
for(int j = 0 ; j <= i ; j++){
if( mapResults->at(it)[toCheck.start+j-1].isReverse == mapResults->at(it)[toCheck.end-i-1].isReverse &&
abs(mapResults->at(it)[toCheck.start+j-1].position - mapResults->at(it)[toCheck.end-i-1].position
- pow(-1,(mapResults->at(it)[toCheck.start+j-1].isReverse==true?1:0))*(toCheck.start+j-(toCheck.end-i))*chunkSize )
<
gapRate*abs(toCheck.start+j-toCheck.end-i) ){
anchoredInterval = interval( toCheck.start+j, toCheck.end-i);
isAnchored = true;
anchorExtendResult = solvedFragInfo(toCheck.start+j,mapResults->at(it)[toCheck.start+j-1].position,
toCheck.end-i, mapResults->at(it)[toCheck.end-i-1].position,
mapResults->at(it)[toCheck.start+j-1].isReverse, it * shiftSteps );
break;
}
}
}
if(isAnchored)
break;
}
}
// =======================
// Check Middle if needed:
if( (toCheck.end-toCheck.start)%2 == 0 && !isAnchored ){
// check Middle with all
long middle = toCheck.start+half-1;
if( mapResults->at(it)[middle].position == 0 )
mapResults->at(it)[middle] = uniqueMap( read->substr((toCheck.start+half-1)*chunkSize, chunkSize)
,qc->substr((toCheck.start+half-1)*chunkSize, chunkSize)
,idx );
if( mapResults->at(it)[middle].position > 0 ){
for (int j = 0; j < half; j++) {
// with left
if( mapResults->at(it)[toCheck.start+j-1].isReverse == mapResults->at(it)[middle].isReverse &&
abs(mapResults->at(it)[toCheck.start+j-1].position - mapResults->at(it)[middle].position
- pow(-1,(mapResults->at(it)[toCheck.start+j-1].isReverse==true?1:0))*(toCheck.start+j-middle)*chunkSize )
<
gapRate*abs(j-middle) ){
anchoredInterval = interval( toCheck.start+j, middle);
isAnchored = true;
anchorExtendResult = solvedFragInfo(toCheck.start+j,mapResults->at(it)[toCheck.start+j-1].position,
middle, mapResults->at(it)[middle].position,
mapResults->at(it)[toCheck.start+j-1].isReverse, it * shiftSteps );
break;
}
//with right
if( mapResults->at(it)[toCheck.end-j-1].isReverse == mapResults->at(it)[middle].isReverse &&
abs(mapResults->at(it)[toCheck.end-j-1].position - mapResults->at(it)[middle].position
- pow(-1,(mapResults->at(it)[toCheck.end-j-1].isReverse==true?1:0))*(toCheck.end-j-middle)*chunkSize )
<
gapRate*abs(j-middle) ){
anchoredInterval = interval( middle, toCheck.end-j);
isAnchored = true;
anchorExtendResult = solvedFragInfo(toCheck.end-j,mapResults->at(it)[toCheck.end-j-1].position,
middle, mapResults->at(it)[middle].position,
mapResults->at(it)[toCheck.end-j-1].isReverse, it * shiftSteps );
break;
}
}
}
}
// ========================
// Recursivley Check Sides:
if( !isAnchored ){
interval tempa = interval(toCheck.start,toCheck.start+half-(1) );
if( abs(tempa.start - tempa.end) > 0 )
checkStack->push_back( tempa );
interval tempb = interval(toCheck.end-half+(1) , toCheck.end );
if( abs(tempb.start - tempb.end) > 0)
checkStack->push_back( tempb );
return interval(0,0);
}
// ONLY Extend-needed ANCHORED Intervals:
// =====================
// Extend if Possible: (only to check intervals)
//1: inExtend
// not yet
if( inClustersExtension ){
// to find in-place balanced structual variations or in aggregation balancer SVs in lng reads...
// extendManager(long from, long until, string* read, solvedFragInfo* anchorExtendResult)
if( false ){
}
// if(BGChangesOnAnchor){
// }
}
//2.a: outExtend left
// if(anchoredInterval.start != toCheck.start ){
// extendedInterval.start = extendManager( anchoredInterval.start, toCheck.start, read, &anchorExtendResult);
// // push unsolved regions:
// if((extendedInterval.start - toCheck.start) > 1)
// checkStack->push_back( interval(toCheck.start, extendedInterval.start-1) );
// }else
// extendedInterval.start = toCheck.start;
// //2.b: outExtend right
// if(anchoredInterval.end != toCheck.end ){
// extendedInterval.end = extendManager( anchoredInterval.end, toCheck.end, read, &anchorExtendResult);
// // push unsolved regions:
// if((toCheck.end - extendedInterval.end) > 1)
// checkStack->push_back( interval(extendedInterval.end+1, toCheck.end) );
// }else
// extendedInterval.end = toCheck.end;
// =====================
// return solved interval
if(isAnchored)
clusters->push_back(anchorExtendResult);
//return extendedInterval;
return anchoredInterval;
}
void inline determineCheckStack( array<vector<bool>, MAX_SHIFT_ITER>* isSolvedChunk , int it,
array<vector<mapResult>, MAX_SHIFT_ITER>* mapResults){
int shiftLen = it*shiftSteps;
// previous chunkings: 0 to it in isSolvedChunk
// nothing yet
}
void buildUpEvents(){
vector<feasibleEvents> debug_rightE(rightE);
vector<feasibleEvents> debug_leftE(leftE);
feasibleEvents tempRight;
tempRight.informatives.push_back( informativeChunk("fake",0,0,0,0,0) );
feasibleEvents tempLeft;
tempLeft.informatives.push_back( informativeChunk("fake",0,0,0,0,0) );
int depcntr = 0;
vector<informativeChunk> infos(informativeChunks);
sort( informativeChunks.begin(), informativeChunks.end() );
sort( infos.begin(), infos.end() );
for(vector<informativeChunk>::iterator it = informativeChunks.begin() ; it != informativeChunks.end(); ++it){
informativeChunk ttemp;
if(it->loci == 2758090 ){
ttemp = *it;
}
if(it->readName == "r2758129++430654^" || it->readName == "r2758136++291071^" || it->readName == "^r2758166++438208^" ){
ttemp = *it;
}
if(it->bpIsRight){
if( tempRight.informatives.back().loci + chunkSize >= it->loci ){
depcntr = 0;
tempRight.informatives.push_back( informativeChunk(*it) );
for(int k = tempRight.informatives.size()-1 ; k >= 0 ; k-- )
if( tempRight.informatives[k].loci+chunkSize >= it->loci )
depcntr++;
else
break;
if( depcntr > tempRight.maxDepth )
tempRight.maxDepth = depcntr;
}else{
//tempRight.informatives.erase( tempRight.informatives.begin() );
tempRight.start = tempRight.informatives[0].loci;
tempRight.end = tempRight.informatives.back().loci+chunkSize;
rightE.push_back(tempRight);
tempRight.informatives.clear();
tempRight.informatives.push_back( informativeChunk(*it) );
tempRight.maxDepth = 1 ;
}
}
else{
if( tempLeft.informatives.back().loci + chunkSize >= it->loci ){
depcntr = 0;
tempLeft.informatives.push_back( informativeChunk(*it) );
for(int k = tempLeft.informatives.size()-1 ; k >= 0 ; k-- )
if( tempLeft.informatives[k].loci+chunkSize >= it->loci )
depcntr++;
else
break;
if( depcntr > tempLeft.maxDepth )
tempLeft.maxDepth = depcntr;
}else{
//tempLeft.informatives.erase( tempLeft.informatives.begin() );
tempLeft.start = tempLeft.informatives[0].loci;
tempLeft.end = tempLeft.informatives.back().loci+chunkSize;
leftE.push_back(tempLeft);
tempLeft.informatives.clear();
tempLeft.informatives.push_back( informativeChunk(*it) );
tempLeft.maxDepth = 1 ;
}
}
}
cerr<<"\n # RightBP Events: "<<rightE.size()<<endl;
cerr<<"\n # LeftBP Events: "<<leftE.size()<<endl;
vector<feasibleEvents> debug_rightE2(rightE);
vector<feasibleEvents> debug_leftE2(leftE);
rightE.front().informatives.erase( rightE.front().informatives.begin() );
if(rightE.front().informatives.size() == 0 )
rightE.erase(rightE.begin());
leftE.front( ).informatives.erase( leftE.front( ).informatives.begin() );
if(leftE.front().informatives.size() == 0 )
leftE.erase(leftE.begin());
informativeChunks.clear();
vector<feasibleEvents> debug_rightE3(rightE);
vector<feasibleEvents> debug_leftE3(leftE);
int a;
}
void debbuildConnections(){
vector<feasibleEvents> debug_rightE(rightE);
vector<feasibleEvents> debug_leftE(leftE);
// r2758129++430654^
// r2758136++291071^
// r2758166++438208^
for(vector<feasibleEvents>::iterator it = debug_rightE.begin() ; it != debug_rightE.end(); ++it){
feasibleEvents tempor(*it);
if(it->start > 46000000)
cerr<<"are";
sort(tempor.informatives.begin(),tempor.informatives.end(),compConnected);
sort(it->informatives.begin(), it->informatives.end(), compConnected);
int index = 0 ;
for( long long i = 0 ; i < debug_rightE.size(); i++ ){
while( (!it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
if( it->informatives[ index ].related_loci >= debug_rightE[i].start
&&
it->informatives[ index ].related_loci <= debug_rightE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,true,1) );
index++;
while( (!it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
while( it->informatives[ index ].related_loci >= debug_rightE[i].start
&&
it->informatives[ index ].related_loci <= debug_rightE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( (!it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
}
if(index >= it->informatives.size() )
break;
}
}
index = 0 ;
for( long long i = 0 ; i < debug_leftE.size(); i++ ){
while( (it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
if( it->informatives[ index ].related_loci >= debug_leftE[i].start
&&
it->informatives[ index ].related_loci <= debug_leftE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,false,1) );
index++;
while( (it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
while( it->informatives[ index ].related_loci >= debug_leftE[i].start
&&
it->informatives[ index ].related_loci <= debug_leftE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( (it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci))
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
}
if(index >= it->informatives.size() )
break;
}
}
}
for(vector<feasibleEvents>::iterator it = debug_leftE.begin() ; it != debug_leftE.end(); ++it){
if(it->start > 46000000)
cerr<<"are";
sort(it->informatives.begin(), it->informatives.end(), compConnected);
int index = 0 ;
for( long long i = 0 ; i < debug_rightE.size(); i++ ){
while( (!it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
if( it->informatives[ index ].related_loci >= debug_rightE[i].start
&&
it->informatives[ index ].related_loci <= debug_rightE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,true,1) );
index++;
while( (!it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
while( it->informatives[ index ].related_loci >= debug_rightE[i].start
&&
it->informatives[ index ].related_loci <= debug_rightE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( (!it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
}
if(index >= it->informatives.size() )
break;
}
}
index = 0 ;
for( long long i = 0 ; i < debug_leftE.size(); i++ ){
while( (it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
if( it->informatives[ index ].related_loci >= debug_leftE[i].start
&&
it->informatives[ index ].related_loci <= debug_leftE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,false,1) );
index++;
while( (it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
while( it->informatives[ index ].related_loci >= debug_leftE[i].start
&&
it->informatives[ index ].related_loci <= debug_leftE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( (it->informatives[ index ].related_bpIsRight) || (!it->informatives[ index ].related_loci) )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
}
if(index >= it->informatives.size() )
break;
}
}
}
rightE = debug_rightE;
leftE = debug_leftE;
}
void buildConnections(){
vector<feasibleEvents> debug_rightE(rightE);
vector<feasibleEvents> debug_leftE(leftE);
// r2758129++430654^
// r2758136++291071^
// r2758166++438208^
for(vector<feasibleEvents>::iterator it = rightE.begin() ; it != rightE.end(); ++it){
sort(it->informatives.begin(), it->informatives.end(), compConnected);
int index = 0 ;
for( long long i = 0 ; i < rightE.size(); i++ ){
while( ! it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
if( it->informatives[ index ].related_loci >= rightE[i].start
&&
it->informatives[ index ].related_loci <= rightE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,true,1) );
index++;
while( ! it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
while( it->informatives[ index ].related_loci >= rightE[i].start
&&
it->informatives[ index ].related_loci <= rightE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( ! it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
}
if(index >= it->informatives.size() )
break;
}
}
index = 0 ;
for( long long i = 0 ; i < leftE.size(); i++ ){
while( it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
if( it->informatives[ index ].related_loci >= leftE[i].start
&&
it->informatives[ index ].related_loci <= leftE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,false,1) );
index++;
while( it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
while( it->informatives[ index ].related_loci >= leftE[i].start
&&
it->informatives[ index ].related_loci <= leftE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
if(++index >= it->informatives.size() )
break;
if(index >= it->informatives.size() )
break;
}
if(index >= it->informatives.size() )
break;
}
}
}
for(vector<feasibleEvents>::iterator it = leftE.begin() ; it != leftE.end(); ++it){
sort(it->informatives.begin(), it->informatives.end(), compConnected);
int index = 0 ;
for( long long i = 0 ; i < rightE.size(); i++ ){
while( ! it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
index++;
if( it->informatives[ index ].related_loci >= rightE[i].start
&&
it->informatives[ index ].related_loci <= rightE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,true,1) );
index++;
while( ! it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
index++;
while( it->informatives[ index ].related_loci >= rightE[i].start
&&
it->informatives[ index ].related_loci <= rightE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( ! it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
index++;
}
}
}
index = 0 ;
for( long long i = 0 ; i < leftE.size(); i++ ){
while( it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
index++;
if( it->informatives[ index ].related_loci > leftE[i].start
&&
it->informatives[ index ].related_loci < leftE[i].end ){
it->connectedEvents.push_back( connectedEvent(i,false,1) );
index++;
while( it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
index++;
while( it->informatives[ index ].related_loci >= leftE[i].start
&&
it->informatives[ index ].related_loci <= leftE[i].end ){
it->connectedEvents.back().weight++;
index++;
while( it->informatives[ index ].related_bpIsRight || !it->informatives[ index ].related_loci )
index++;
}
}
}
}
vector<feasibleEvents> debug2_rightE(rightE);
vector<feasibleEvents> debug2_leftE(leftE);
}
int overlapsMaxDepth(string which, long long start, long long end){
// WRITE A BETTER ONE... PLEASE.
int overlaps = 0;
if( which == "left" ){
for(vector<feasibleEvents>::iterator it = leftE.begin() ; it != leftE.end(); ++it){
if( (it->start >= start && it->start <= end) || (it->end >= start && it->end <= end) )
overlaps = max( overlaps , it->maxDepth );
}
}else{
for(vector<feasibleEvents>::iterator it = rightE.begin() ; it != rightE.end(); ++it){
if( (it->start >= start && it->start <= end) || (it->end >= start && it->end <= end) )
overlaps = max( overlaps , it->maxDepth );
}
}
return overlaps;
}
double P_reads_BPC( ){
}
double P_BPC_SVType( ){
}
void graphData(){
vector<feasibleEvents> debug_rightE(rightE);
vector<feasibleEvents> debug_leftE(leftE);
// //////////////////////////////////////////////
// ///////// Build Graph /////////
int rightCount = rightE.size();
int nodeCount = rightCount + leftE.size();
int** adjacencyMatrix = new int*[nodeCount];
for(int i = 0; i < nodeCount; ++i)
adjacencyMatrix[i] = new int[nodeCount];
for(int i = 0; i < nodeCount; ++i)
for(int j = 0; j < nodeCount; ++j)
adjacencyMatrix[i][j]=0;
int *nodeLocation[2];
for(int i = 0; i < 2; ++i)
nodeLocation[i] = new int[nodeCount];
for(int i = 0; i < 2; ++i)
for(int j = 0; j < nodeCount; ++j)
nodeLocation[i][j] = 0;
int *nodeWeight = new int[nodeCount];
bool *node_BRIsRight = new bool[nodeCount];
int eveCntr = -1;
for(vector<feasibleEvents>::iterator it = rightE.begin() ; it != rightE.end(); ++it){
eveCntr++;
nodeLocation[0][eveCntr] = (it->start);
nodeLocation[1][eveCntr] = (it->end);
node_BRIsRight[eveCntr] = true;
nodeWeight[eveCntr] = it->informatives.size();
for(int i = 0 ; i < it->connectedEvents.size() ; i++ ){
adjacencyMatrix[eveCntr][it->connectedEvents[i].index+(it->connectedEvents[i].isRightBP?0:rightCount)]
+= it->connectedEvents[i].weight ;
}
}
for(vector<feasibleEvents>::iterator it = leftE.begin() ; it != leftE.end(); ++it){
eveCntr++;
nodeLocation[0][eveCntr] = (it->start);
nodeLocation[1][eveCntr] = (it->end);
node_BRIsRight[eveCntr] = false;
nodeWeight[eveCntr] = it->informatives.size();
for(int i = 0 ; i < it->connectedEvents.size() ; i++ ){
adjacencyMatrix[eveCntr][(it->connectedEvents[i].index)+(it->connectedEvents[i].isRightBP?0:rightCount)]
+= it->connectedEvents[i].weight;
}
}
// //////////////////////////////////////////////
// ///////// Write Graph /////////
int a;
ofstre_graphData<<"From+1\tTo+1\tWeight"<<endl;
for(int i = 0; i < nodeCount; ++i)
for(int j = 0; j < nodeCount; ++j)
if(adjacencyMatrix[i][j] != 0){
a = adjacencyMatrix[i][j];
ofstre_graphData<<(i+1)<<"\t"<<(j+1)<<"\t"<<adjacencyMatrix[i][j]<<"\n";
//ofstre_graphData<<"("<<i<<","<<j<<"):"<<adjacencyMatrix[i][j]<<"\n";
}
else
;
ofstre_graphData2<<"Start\tEnd\tWeight\tBreakPoint"<<endl;
for(int j = 0; j < nodeCount; ++j)
ofstre_graphData2<<nodeLocation[0][j]<<"\t"<<nodeLocation[1][j]<<"\t"
<<nodeWeight[j]<<"\t"<<(node_BRIsRight?"BRIsRight (+1)":"BRIsLeft (-1)")<<endl;
// for(int j = 0; j < nodeCount; ++j)
// ofstre_graphData3<<nodeWeight[j]<<"\n";
ofstre_graphData.close();
ofstre_graphData2.close();
ofstre_graphData3.close();
// //////////////////////////////////////////////////////////////////
// ///////// Build Graph with adjacency list /////////
graph AdjaList;
AdjaList.buildFromMatrices( adjacencyMatrix, nodeCount, nodeWeight, nodeLocation, node_BPIsRight);
AdjaList.overlappedConnector();
// //////////////////////////////////////////////
// ///////// Motif Finding /////////
}
void writeEvents(){
vector<feasibleEvents> debug_rightE(rightE);
vector<feasibleEvents> debug_leftE(leftE);
ofstre_rightEvents<<"#E\tStart..\tEnd...\tMaxDepth\t#Informatives\t|\tConnections(index-weight-lef/right BP)"<<endl<<"_____________________________________"<<endl;
int eveCntr = -1;
for(vector<feasibleEvents>::iterator it = rightE.begin() ; it != rightE.end(); ++it){
eveCntr++;
if( (it->maxDepth + overlapsMaxDepth("left",it->start,it->end) > MINACCEVENTDEPTH) || it->connectedEvents.size() > 0 ){
ofstre_rightEvents<<eveCntr<<":\t"<<it->start<<"\t"<<it->end<<"\t"<<it->maxDepth<<"\t"<<it->informatives.size()<<"\t|";
for(int i = 0 ; i < (it->connectedEvents.size()<3?it->connectedEvents.size():3) ; i++ )
ofstre_rightEvents<<"\t"<<it->connectedEvents[i].index<<"\t"<<it->connectedEvents[i].weight<<"\t"<<(it->connectedEvents[i].isRightBP?"\-\> |":"\<\- |");
ofstre_rightEvents<<endl;
bool writeReadNames = true;
if(writeReadNames){
ofstre_rightEvents<<"readNames:\n";
for(int i = 0 ; i < it->informatives.size() ; i++ ){
ofstre_rightEvents<<it->informatives[i].readName;
}
ofstre_rightEvents<<endl<<"_____________________________________"<<endl;
}
}
}
eveCntr = -1;
ofstre_leftEvents<<"#E\tStart..\tEnd...\tMaxDepth\t#Informatives\t|\tConnections(index-weight-lef/right BP)"<<endl<<"_____________________________________"<<endl;
for(vector<feasibleEvents>::iterator it = leftE.begin() ; it != leftE.end(); ++it){
eveCntr++;
if( (it->maxDepth + overlapsMaxDepth("right",it->start,it->end) > MINACCEVENTDEPTH) || it->connectedEvents.size() > 0 ){
int aaa = overlapsMaxDepth("right",it->start,it->end);
//cerr<<it->maxDepth<<" "<<overlapsMaxDepth("right",it->start,it->end)<<" "<<it->start<<" "<< it->end <<endl;
ofstre_leftEvents<<eveCntr<<":\t"<<it->start<<"\t"<<it->end<<"\t"<<it->maxDepth<<"\t"<<it->informatives.size()<<"\t|";
for(int i = 0 ; i < (it->connectedEvents.size()<3?it->connectedEvents.size():3) ; i++ )
ofstre_leftEvents<<"\t"<<it->connectedEvents[i].index<<"\t"<<it->connectedEvents[i].weight<<"\t"<<(it->connectedEvents[i].isRightBP?"\-\> |":"\<\- |");
ofstre_leftEvents<<endl;
bool writeReadNames = true;
if(writeReadNames){
ofstre_leftEvents<<"readNames:\n";
for(int i = 0 ; i < it->informatives.size() ; i++ ){