void test_addOutEdge(){
string a="CAATAAGTAAAAAAGATTTTGTAACTTTCACAGCCTTATTTTTATCAATAGATACTGATAT";
string b= "AATAAGTAAAAAAGATTTTGTAACTTTCACAGCCTTATTTTTATCAATAGATACTGATATT";
int wordSize=a.length();
Kmer aKmer=wordId(a.c_str());
Kmer bKmer=wordId(b.c_str());
Vertex aVertex;
aVertex.constructor();
Kmer lower=aKmer;
Kmer aRC=aKmer.complementVertex(wordSize,false);
if(aRC<lower){
lower=aRC;
}
aVertex.m_lowerKey=lower;
aVertex.addOutgoingEdge(&aKmer,&bKmer,wordSize);
vector<Kmer>Edges=aVertex.getOutgoingEdges(&aKmer,wordSize);
bool found=false;
for(int j=0;j<(int)Edges.size();j++){
if(Edges[j]==bKmer){
found=true;
break;
}
}
if(!found){
cout<<"Expected: "<<endl;
cout<<b<<endl;
cout<<"Actual:"<<endl;
for(int j=0;j<(int)Edges.size();j++){
cout<<Edges[j].idToWord(wordSize,false)<<endl;
}
uint8_t edges=aVertex.getEdges(&aKmer);
cout<<"Edges"<<endl;
print8(edges);
}
assertEquals(Edges.size(),1);
assertEquals(found,true);
}
void GenomeGraphReader::readLine() {
char buffer[1024];
buffer[0] = '\0';
bool isCurrentlyAtTheGreatEndOfTime = m_reader.eof();
while(!m_bad && !m_reader.eof()) {
m_reader.getline(buffer, 1024);
// skip comment
if(strlen(buffer) > 0 && buffer[0] == '#')
continue;
break;
}
if(m_bad || (m_reader.eof() && isCurrentlyAtTheGreatEndOfTime)) {
m_reader.close();
printName();
if(m_bad) {
cout << " Error: file " << m_fileName << " does not exist";
cout << endl;
} else {
cout << " finished reading file " << m_fileName;
cout << " got " << m_loaded << " objects" << endl;
}
Message finishedMessage;
finishedMessage.setTag(DONE);
send(m_parent, finishedMessage);
die();
} else {
// AGCTGTGAAACTGGTGCAAGCTACCAGAATC;36;A;C
string sequence;
CoverageDepth coverage;
string parents;
string children;
for(int i = 0 ; i < (int) strlen(buffer) ; ++i) {
if(buffer[i] == ';')
buffer[i] = ' ';
}
istringstream stringBuffer(buffer);
stringBuffer >> sequence;
stringBuffer >> coverage;
stringBuffer >> parents;
stringBuffer >> children;
///////////////////////////////////////////////////////////////////////
// convert the sequence to upper case
map<char,char> translationTable;
translationTable['a'] = 'A';
translationTable['t'] = 'T';
translationTable['g'] = 'G';
translationTable['c'] = 'C';
for(int i = 0 ; i < (int) sequence.length() ; ++i) {
char symbol = sequence[i];
if(translationTable.count(symbol) > 0) {
char correct = translationTable[symbol];
sequence [i] = correct;
}
}
#if 0
cout << "DEBUG " << sequence << " with " << coverage << endl;
#endif
// if this is the first one, send the k-mer length too
if(m_loaded == 0) {
Message aMessage;
aMessage.setTag(CoalescenceManager::SET_KMER_LENGTH);
int length = sequence.length();
aMessage.setBuffer(&length);
aMessage.setNumberOfBytes(sizeof(length));
send(m_aggregator, aMessage);
}
Kmer kmer;
kmer.loadFromTextRepresentation(sequence.c_str());
Vertex vertex;
vertex.setKey(kmer);
vertex.setCoverageValue(coverage);
// add parents
for(int i = 0 ; i < (int)parents.length() ; ++i) {
string parent = sequence;
for(int j = 0 ; j < (int) parent.length()-1 ; ++j) {
parent[j + 1] = parent[j];
}
parent[0] = parents[i];
Kmer parentKmer;
parentKmer.loadFromTextRepresentation(parent.c_str());
vertex.addIngoingEdge(&kmer, &parentKmer, sequence.length());
}
// add children
for(int i = 0 ; i < (int)children.length() ; ++i) {
string child = sequence;
for(int j = 0 ; j < (int) child.length()-1 ; ++j) {
child[j] = child[j + 1];
}
child[child.length() - 1] = children[i];
Kmer childKmer;
childKmer.loadFromTextRepresentation(child.c_str());
vertex.addOutgoingEdge(&kmer, &childKmer, sequence.length());
}
char messageBuffer[100];
int position = 0;
position += vertex.dump(messageBuffer + position);
memcpy(messageBuffer + position, &m_sample, sizeof(m_sample));
position += sizeof(m_sample);
// maybe: accumulate many objects before flushing it.
// we can go up to MAXIMUM_MESSAGE_SIZE_IN_BYTES bytes.
/*
printName();
cout << " got data line " << buffer;
cout << " sending PAYLOAD to " << m_aggregator << endl;
*/
Message message;
message.setTag(CoalescenceManager::PAYLOAD);
message.setBuffer(messageBuffer);
message.setNumberOfBytes(position);
#if 0
printName();
cout << "DEBUG sending PAYLOAD to " << m_aggregator;
cout << " with " << position << " bytes ";
vertex.print(sequence.length(), false);
cout << endl;
#endif
int period = 1000000;
if(m_loaded % period == 0) {
printName();
cout << " loaded " << m_loaded << " sequences" << endl;
}
m_loaded ++;
send(m_aggregator, message);
}
}
