void GraphPath::push_back(const Kmer*a){
#ifdef ASSERT
assert(m_kmerLength!=0);
#endif
if(!canBeAdded(a)){
if(!m_errorRaised){
cout<<"Error: can not add "<<a->idToWord(m_kmerLength,false)<<endl;
cout<<"last objects:"<<endl;
int count=16;
int iterator=size()-count;
while(iterator<size()){
Kmer theObject;
at(iterator,&theObject);
cout<<" ["<<iterator<<"] ------> "<<theObject.idToWord(m_kmerLength,false)<<endl;
iterator++;
}
m_errorRaised=true;
}
return;
}
#ifdef CONFIG_PATH_STORAGE_DEFAULT
m_vertices.push_back(*a);
#elif defined(CONFIG_PATH_STORAGE_BLOCK)
writeObjectInBlock(a);
#endif
}
void BubbleTool::printStuff(Kmer root,vector<vector<Kmer> >*trees,
map<Kmer,int>*coverages){
int m_wordSize=m_parameters->getWordSize();
cout<<"Trees="<<trees->size()<<endl;
cout<<"root="<<root.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<endl;
cout<<"digraph{"<<endl;
map<Kmer,set<Kmer> > printedEdges;
for(map<Kmer ,int>::iterator i=coverages->begin();i!=coverages->end();i++){
Kmer kmer=i->first;
cout<<kmer.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<" [label=\""<<kmer.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<" "<<i->second<<"\"]"<<endl;
}
for(int j=0;j<(int)trees->size();j++){
for(int i=0;i<(int)trees->at(j).size();i+=2){
Kmer a=trees->at(j).at(i+0);
#ifdef ASSERT
assert(i+1<(int)trees->at(j).size());
#endif
Kmer b=trees->at(j).at(i+1);
if(printedEdges.count(a)>0 && printedEdges[a].count(b)>0){
continue;
}
cout<<a.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<" -> "<<b.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<endl;
printedEdges[a].insert(b);
}
}
cout<<"}"<<endl;
}
void GraphPath::writeObjectInBlock(const Kmer*a){
#ifdef ASSERT
assert(m_kmerLength!=0);
#endif
#ifdef CHECK_BUG_142
string copyA="AGGAAGAACCTGCTGAGGAACAAGAAGGTCAACTGCCTGGACTGTAATACC";
string copyB=a->idToWord(m_kmerLength,false);
if(copyA==copyB)
cout<<"[GraphPath::writeObjectInBlock] returns "<<copyB<<endl;
#endif
if(m_size==0){
#ifdef ASSERT
assert(m_blocks.size()==0);
#endif
addBlock();
string sequence=a->idToWord(m_kmerLength,false);
for(int blockPosition=0;blockPosition<m_kmerLength;blockPosition++){
writeSymbolInBlock(blockPosition,sequence[blockPosition]);
}
}else{
#ifdef ASSERT
assert(m_size>=1);
assert(a!=NULL);
assert(m_kmerLength!=0);
#endif
char lastSymbol=a->getLastSymbol(m_kmerLength,false);
int usedSymbols=size()+m_kmerLength-1;
#ifdef ASSERT
assert(usedSymbols>=m_kmerLength);
assert(m_blocks.size()>=1);
#endif
int allocatedSymbols=m_blocks.size()*getBlockSize();
#ifdef ASSERT
assert(allocatedSymbols>=getBlockSize());
#endif
if(usedSymbols+1>allocatedSymbols){
addBlock();
allocatedSymbols=m_blocks.size()*getBlockSize();
}
#ifdef ASSERT
assert(usedSymbols+1<=allocatedSymbols);
assert(allocatedSymbols>=getBlockSize());
#endif
int position=usedSymbols;
#ifdef ASSERT
assert(position<allocatedSymbols);
#endif
writeSymbolInBlock(position,lastSymbol);
}
m_size++;
#ifdef ASSERT
Kmer addedObject;
at(size()-1,&addedObject);
if((*a)!=addedObject){
cout<<"Error: expected: "<<a->idToWord(m_kmerLength,false)<<endl;
cout<<"actual: "<<addedObject.idToWord(m_kmerLength,false)<<" at position "<<size()-1<<endl;
cout<<"kmerLength: "<<m_kmerLength<<" blockSize: "<<getBlockSize()<<endl;
int i=size()-1;
int j=0;
cout<<"dump:"<<endl;
while(i-j>=0 && j<10){
Kmer theObject;
at(i-j,&theObject);
cout<<" ["<<i-j<<"] ------> "<<theObject.idToWord(m_kmerLength,false)<<endl;
j++;
}
}
assert((*a)==addedObject);
#endif
}
/*
* do a depth first search with max depth of maxDepth;
*/
void DepthFirstSearchData::depthFirstSearch(Kmer root,Kmer a,int maxDepth,
bool*edgesRequested,bool*vertexCoverageRequested,bool*vertexCoverageReceived,
RingAllocator*outboxAllocator,int size,int theRank,StaticVector*outbox,
int*receivedVertexCoverage,vector<Kmer>*receivedOutgoingEdges,
int minimumCoverage,bool*edgesReceived,int wordSize,Parameters*parameters) {
if(!m_doChoice_tips_dfs_initiated) {
m_depthFirstSearchVisitedVertices.clear();
m_depthFirstSearchVisitedVertices_vector.clear();
// add an arc
m_depthFirstSearchVisitedVertices_vector.push_back(root);
m_depthFirstSearchVisitedVertices_vector.push_back(a);
m_depthFirstSearchVisitedVertices_depths.clear();
while(m_depthFirstSearchVerticesToVisit.size()>0) {
m_depthFirstSearchVerticesToVisit.pop();
}
while(m_depthFirstSearchDepths.size()>0) {
m_depthFirstSearchDepths.pop();
}
m_maxDepthReached=false;
m_depthFirstSearchVerticesToVisit.push(a);
m_depthFirstSearchVisitedVertices.insert(a);
m_depthFirstSearchDepths.push(0);
m_depthFirstSearch_maxDepth=0;
m_doChoice_tips_dfs_initiated=true;
m_doChoice_tips_dfs_done=false;
m_coverages.clear();
(*edgesRequested)=false;
(*vertexCoverageRequested)=false;
#ifdef SHOW_MINI_GRAPH
cout<<"<MiniGraph>"<<endl;
cout<<root->idToWord(wordSize,parameters->getColorSpaceMode())<<" -> "<<a->idToWord(wordSize,parameters->getColorSpaceMode())<<endl;
#endif
}
if(m_depthFirstSearchVerticesToVisit.size()>0) {
Kmer vertexToVisit=m_depthFirstSearchVerticesToVisit.top();
if(!(*vertexCoverageRequested)) {
(*vertexCoverageRequested)=true;
(*vertexCoverageReceived)=false;
MessageUnit*message=(MessageUnit*)(*outboxAllocator).allocate(KMER_U64_ARRAY_SIZE*sizeof(MessageUnit));
int j=0;
vertexToVisit.pack(message,&j);
int dest=parameters->vertexRank(&vertexToVisit);
Message aMessage(message,j,dest,RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE,theRank);
(*outbox).push_back(&aMessage);
} else if((*vertexCoverageReceived)) {
if(!(*edgesRequested)) {
m_coverages[vertexToVisit]=(*receivedVertexCoverage);
m_depthFirstSearchVisitedVertices.insert(vertexToVisit);
int theDepth=m_depthFirstSearchDepths.top();
if(theDepth> m_depthFirstSearch_maxDepth) {
m_depthFirstSearch_maxDepth=theDepth;
}
// visit the vertex, and ask next edges.
MessageUnit*message=(MessageUnit*)(*outboxAllocator).allocate(1*sizeof(MessageUnit));
int bufferPosition=0;
vertexToVisit.pack(message,&bufferPosition);
int destination=parameters->vertexRank(&vertexToVisit);
Message aMessage(message,bufferPosition,destination,RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES,theRank);
(*outbox).push_back(&aMessage);
(*edgesRequested)=true;
(*edgesReceived)=false;
} else if((*edgesReceived)) {
Kmer vertexToVisit=m_depthFirstSearchVerticesToVisit.top();
int theDepth=m_depthFirstSearchDepths.top();
#ifdef ASSERT
assert(theDepth>=0);
assert(theDepth<=maxDepth);
#endif
int newDepth=theDepth+1;
m_depthFirstSearchVerticesToVisit.pop();
m_depthFirstSearchDepths.pop();
for(int i=0; i<(int)(*receivedOutgoingEdges).size(); i++) {
Kmer nextVertex=(*receivedOutgoingEdges)[i];
if(m_depthFirstSearchVisitedVertices.count(nextVertex)>0) {
continue;
}
if(newDepth>maxDepth) {
m_maxDepthReached=true;
continue;
}
if(m_depthFirstSearchVisitedVertices.size()<MAX_VERTICES_TO_VISIT) {
// add an arc
m_depthFirstSearchVisitedVertices_vector.push_back(vertexToVisit);
m_depthFirstSearchVisitedVertices_vector.push_back(nextVertex);
// add the depth for the vertex
m_depthFirstSearchVisitedVertices_depths.push_back(newDepth);
// stacks
m_depthFirstSearchVerticesToVisit.push(nextVertex);
m_depthFirstSearchDepths.push(newDepth);
}
#ifdef SHOW_MINI_GRAPH
cout<<vertexToVisit->idToWord(wordSize,parameters->getColorSpaceMode())<<" -> "<<nextVertex->idToWord(wordSize,parameters->getColorSpaceMode())<<endl;
#endif
}
(*edgesRequested)=false;
(*vertexCoverageRequested)=false;
}
}
} else {
m_doChoice_tips_dfs_done=true;
#ifdef SHOW_MINI_GRAPH
cout<<"</MiniGraph>"<<endl;
#endif
}
}
void DepthFirstSearchData::depthFirstSearchBidirectional(Kmer a,int maxDepth,
bool*edgesRequested,bool*vertexCoverageRequested,bool*vertexCoverageReceived,
RingAllocator*outboxAllocator,int size,int theRank,StaticVector*outbox,
int*receivedVertexCoverage,SeedingData*seedingData,
int minimumCoverage,bool*edgesReceived,Parameters*parameters) {
#ifdef ASSERT
int wordSize=parameters->getWordSize();
#endif
if(!m_doChoice_tips_dfs_initiated) {
m_outgoingEdges.clear();
m_ingoingEdges.clear();
m_depthFirstSearchVisitedVertices.clear();
m_depthFirstSearchVisitedVertices_vector.clear();
m_depthFirstSearchVisitedVertices_depths.clear();
while(m_depthFirstSearchVerticesToVisit.size()>0) {
m_depthFirstSearchVerticesToVisit.pop();
}
while(m_depthFirstSearchDepths.size()>0) {
m_depthFirstSearchDepths.pop();
}
m_maxDepthReached=false;
m_depthFirstSearchVerticesToVisit.push(a);
m_depthFirstSearchDepths.push(0);
m_depthFirstSearch_maxDepth=0;
m_doChoice_tips_dfs_initiated=true;
m_doChoice_tips_dfs_done=false;
m_coverages.clear();
(*edgesRequested)=false;
(*vertexCoverageRequested)=false;
}
if(m_depthFirstSearchVerticesToVisit.size()>0) {
Kmer vertexToVisit=m_depthFirstSearchVerticesToVisit.top();
if(!(*vertexCoverageRequested)) {
if(m_depthFirstSearchVisitedVertices.count(vertexToVisit)>0) {
m_depthFirstSearchVerticesToVisit.pop();
m_depthFirstSearchDepths.pop();
return;
}
(*vertexCoverageRequested)=true;
(*vertexCoverageReceived)=false;
MessageUnit*message=(MessageUnit*)(*outboxAllocator).allocate(KMER_U64_ARRAY_SIZE*sizeof(MessageUnit));
int bufferPosition=0;
vertexToVisit.pack(message,&bufferPosition);
int dest=parameters->vertexRank(&vertexToVisit);
Message aMessage(message,bufferPosition,dest,RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE,theRank);
(*outbox).push_back(&aMessage);
} else if((*vertexCoverageReceived)) {
if(!(*edgesRequested)) {
m_coverages[vertexToVisit]=(*receivedVertexCoverage);
#ifdef ASSERT
if(m_depthFirstSearchVisitedVertices.count(vertexToVisit)>0) {
cout<<"Already visited: "<<vertexToVisit.idToWord(wordSize,parameters->getColorSpaceMode())<<" root is "<<a.idToWord(wordSize,parameters->getColorSpaceMode())<<endl;
}
assert(m_depthFirstSearchVisitedVertices.count(vertexToVisit)==0);
assert(*receivedVertexCoverage>0);
#endif
if((*receivedVertexCoverage)>0) {
m_depthFirstSearchVisitedVertices.insert(vertexToVisit);
} else {
#ifdef ASSERT
assert(false);
#endif
// don't visit it.
m_depthFirstSearchVerticesToVisit.pop();
m_depthFirstSearchDepths.pop();
(*edgesRequested)=false;
(*vertexCoverageRequested)=false;
return;
}
int theDepth=m_depthFirstSearchDepths.top();
if(theDepth> m_depthFirstSearch_maxDepth) {
m_depthFirstSearch_maxDepth=theDepth;
}
// visit the vertex, and ask next edges.
MessageUnit*message=(MessageUnit*)(*outboxAllocator).allocate(1*sizeof(MessageUnit));
int bufferPosition=0;
vertexToVisit.pack(message,&bufferPosition);
int destination=parameters->vertexRank(&vertexToVisit);
Message aMessage(message,bufferPosition,destination,RAY_MPI_TAG_REQUEST_VERTEX_EDGES,theRank);
(*outbox).push_back(&aMessage);
(*edgesRequested)=true;
(*edgesReceived)=false;
} else if((*edgesReceived)) {
Kmer vertexToVisit=m_depthFirstSearchVerticesToVisit.top();
int theDepth=m_depthFirstSearchDepths.top();
#ifdef ASSERT
assert(theDepth>=0);
assert(theDepth<=maxDepth);
#endif
int newDepth=theDepth+1;
m_depthFirstSearchVerticesToVisit.pop();
m_depthFirstSearchDepths.pop();
// the first 4 elements are padding
// the 5th is the number of outgoing edges
// following are the outgoing edges
// following is the number of ingoing edges
// following are the ingoing edges.
vector<Kmer > outgoingEdges=seedingData->m_SEEDING_receivedOutgoingEdges;
for(int i=0; i<(int)outgoingEdges.size(); i++) {
Kmer nextVertex=outgoingEdges[i];
if(m_depthFirstSearchVisitedVertices.size()>=MAX_VERTICES_TO_VISIT) {
continue;
}
if(m_depthFirstSearchVisitedVertices.count(nextVertex)>0) {
continue;
}
if(newDepth>maxDepth) {
m_maxDepthReached=true;
continue;
}
m_depthFirstSearchVerticesToVisit.push(nextVertex);
m_depthFirstSearchDepths.push(newDepth);
m_depthFirstSearchVisitedVertices_vector.push_back(vertexToVisit);
m_depthFirstSearchVisitedVertices_vector.push_back(nextVertex);
m_depthFirstSearchVisitedVertices_depths.push_back(newDepth);
}
#ifdef ASSERT
if(m_outgoingEdges.count(vertexToVisit)>0) {
cout<<vertexToVisit.idToWord(wordSize,parameters->getColorSpaceMode())<<" is already in the data structure "<<m_outgoingEdges[vertexToVisit].size()<<" v. "<<outgoingEdges.size()<<endl;
}
assert(m_outgoingEdges.count(vertexToVisit)==0);
#endif
m_outgoingEdges[vertexToVisit]=outgoingEdges;
vector<Kmer> ingoingEdges=seedingData->m_SEEDING_receivedIngoingEdges;
for(int i=0; i<(int)ingoingEdges.size(); i++) {
Kmer nextVertex=ingoingEdges[i];
if(m_depthFirstSearchVisitedVertices.size()>=MAX_VERTICES_TO_VISIT) {
continue;
}
if(m_depthFirstSearchVisitedVertices.count(nextVertex)>0) {
continue;
}
if(newDepth>maxDepth) {
m_maxDepthReached=true;
continue;
}
m_depthFirstSearchVerticesToVisit.push(nextVertex);
m_depthFirstSearchDepths.push(newDepth);
// reverse the order.
m_depthFirstSearchVisitedVertices_vector.push_back(nextVertex);
m_depthFirstSearchVisitedVertices_vector.push_back(vertexToVisit);
m_depthFirstSearchVisitedVertices_depths.push_back(newDepth);
}
(*edgesRequested)=false;
(*vertexCoverageRequested)=false;
#ifdef ASSERT
assert(m_ingoingEdges.count(vertexToVisit)==0);
#endif
m_ingoingEdges[vertexToVisit]=ingoingEdges;
}
}
} else {
m_doChoice_tips_dfs_done=true;
#ifdef SHOW_MINI_GRAPH
cout<<"</MiniGraph>"<<endl;
#endif
}
}
bool BubbleTool::isGenuineBubble(Kmer root,vector<vector<Kmer > >*trees,
map<Kmer ,int>*coverages,int repeatCoverage){
#ifdef NO_BUBBLES
return false;
#endif
if((*coverages)[root]>= repeatCoverage){
return false;
}
int m_wordSize=m_parameters->getWordSize();
#ifdef ASSERT
for(int i=0;i<(int)trees->size();i++){
for(int j=0;j<(int)trees->at(i).size();j+=2){
Kmer a=trees->at(i).at(j+0);
Kmer b=trees->at(i).at(j+1);
string as=a.idToWord(m_wordSize,m_parameters->getColorSpaceMode());
string bs=b.idToWord(m_wordSize,m_parameters->getColorSpaceMode());
assert(as.substr(1,m_wordSize-1)==bs.substr(0,m_wordSize-1));
}
}
#endif
if(m_parameters->debugBubbles()){
printStuff(root,trees,coverages);
}
if(trees->size()!=2){
return false;// we don'T support that right now ! triploid stuff are awesome.
}
// given the word size
// check that they join.
//
// substitution SNP is d=0
// del is 1, 2, or 3
map<Kmer ,int> coveringNumber;
Kmer target;
bool foundTarget=false;
for(int j=0;j<(int)trees->size();j++){
for(int i=0;i<(int)trees->at(j).size();i+=2){
Kmer a=trees->at(j).at(i+1);
#ifdef ASSERT
if(coverages->count(a)==0){
cout<<a.idToWord(m_parameters->getWordSize(),m_parameters->getColorSpaceMode())<<" has no coverage."<<endl;
}
assert(coverages->count(a)>0);
#endif
coveringNumber[a]++;
if(!foundTarget && coveringNumber[a]==2){
foundTarget=true;
target=a;
break;
}
}
}
if(!foundTarget){
if(m_parameters->debugBubbles()){
cout<<"Target not found."<<endl;
}
return false;
}
if((*coverages)[target]>= repeatCoverage){
return false;
}
#ifdef ASSERT
assert(coverages->count(root)>0);
assert(coverages->count(target)>0);
#endif
#ifdef ASSERT
int rootCoverage=(*coverages)[root];
int targetCoverage=(*coverages)[target];
assert(rootCoverage>0);
assert(targetCoverage>0);
#endif
vector<map<Kmer ,Kmer > > parents;
for(int j=0;j<(int)trees->size();j++){
map<Kmer ,Kmer > aVector;
parents.push_back(aVector);
for(int i=0;i<(int)trees->at(j).size();i+=2){
Kmer a=trees->at(j).at(i+0);
Kmer b=trees->at(j).at(i+1);
parents[j][b]=a;
}
}
vector<vector<int> > observedValues;
/*
*
* BUBBLE is below
*
* * ---- * -------* --------*
* \ /
* ---- * --------* ------ *
*
*/
// accumulate observed values
// and stop when encountering
for(int j=0;j<(int)trees->size();j++){
vector<int> aVector;
observedValues.push_back(aVector);
set<Kmer > visited;
Kmer startingPoint=trees->at(j).at(0);
Kmer current=target;
while(current!=startingPoint){
if(visited.count(current)>0){
return false;
}
visited.insert(current);
Kmer theParent=parents[j][current];
int coverageValue=(*coverages)[theParent];
observedValues[j].push_back(coverageValue);
current=theParent;
}
}
if(m_parameters->debugBubbles()){
cout<<"O1="<<observedValues[0].size()<<" O2="<<observedValues[1].size()<<endl;
}
int sum1=0;
for(int i=0;i<(int)observedValues[0].size();i++){
sum1+=observedValues[0][i];
}
if(m_parameters->debugBubbles()){
cout<<"O1Values= ";
for(int i=0;i<(int)observedValues[0].size();i++){
cout<<observedValues[0][i]<<" ";
}
cout<<endl;
}
int sum2=0;
for(int i=0;i<(int)observedValues[1].size();i++){
sum2+=observedValues[1][i];
}
if(m_parameters->debugBubbles()){
cout<<"O2Values= ";
for(int i=0;i<(int)observedValues[1].size();i++){
cout<<observedValues[1][i]<<" ";
}
cout<<endl;
}
if((int)observedValues[0].size()<2*m_parameters->getWordSize()
&& (int)observedValues[1].size()<2*m_parameters->getWordSize()){
if(sum1>sum2){
m_choice=trees->at(0).at(1);
}else if(sum2>sum1){
m_choice=trees->at(1).at(1);
// this will not happen often
}else if(sum1==sum2){
// take the shortest, if any
if(observedValues[0].size()<observedValues[1].size()){
m_choice=trees->at(0).at(1);
}else if(observedValues[1].size()<observedValues[0].size()){
m_choice=trees->at(1).at(1);
// same length and same sum, won't happen very often anyway
}else{
m_choice=trees->at(0).at(1);
}
}
if(m_parameters->debugBubbles()){
cout<<"This is a genuine bubble"<<endl;
cout<<"root="<<root.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<" target="<<target.idToWord(m_wordSize,m_parameters->getColorSpaceMode())<<endl;
}
return true;
}
if(m_parameters->debugBubbles()){
cout<<"False at last"<<endl;
}
return false;
}
