/**
* Get the ingoing edges
* one bit (1=yes, 0=no) per possible edge
*/
vector<Kmer> Kmer::_getIngoingEdges(uint8_t edges,int k){
vector<Kmer> b;
Kmer aTemplate;
aTemplate=*this;
int posToClear=2*k;
for(int i=0;i<aTemplate.getNumberOfU64();i++){
uint64_t element=aTemplate.getU64(i);
element=element<<2;
// 1 0
//
// 127..64 63...0
//
// 00abcdefgh ijklmnopqr // initial state
// abcdefgh00 klmnopqr00 // shift left
// abcdefghij klmnopqr00 // copy the last to the first
// 00cdefghij klmnopqr00 // reset the 2 last
/**
* Now, we need to copy 2 bits from
*/
if(i!=0){
// the 2 last of the previous will be the 2 first of this one
uint64_t last=getU64(i-1);
last=(last>>62);
element=element|last;
}
/**
* The two last bits that shifted must be cleared
* Otherwise, it will change the hash value of the Kmer...
* The chunk number i contains bits from i to i*64-1
* Therefore, if posToClear is inside these boundaries,
* then it is obvious that these awful bits must be changed
* to 0
*/
if(i*64<=posToClear&&posToClear<i*64+64){
int position=posToClear%64;
uint64_t filter=3;// 11 or 1*2^1+1*2^0
filter=filter<<(position);
filter=~filter;
element=element&filter;
}
aTemplate.setU64(i,element);
}
Kmer wordId(const char*a){
Kmer i;
int theLen=strlen(a);
for(int j=0;j<(int)theLen;j++){
uint64_t k=charToCode(a[j]);
int bitPosition=2*j;
int chunk=bitPosition/64;
int bitPositionInChunk=bitPosition%64;
#ifdef ASSERT
if(!(chunk<i.getNumberOfU64())){
cout<<"Chunk="<<chunk<<" positionInKmer="<<j<<" KmerLength="<<strlen(a)<<" bitPosition=" <<bitPosition<<" Chunks="<<i.getNumberOfU64()<<endl;
}
assert(chunk<i.getNumberOfU64());
#endif
uint64_t filter=(k<<bitPositionInChunk);
i.setU64(chunk,i.getU64(chunk)|filter);
}
return i;
}
/**
* Get the outgoing edges
* one bit (1=yes, 0=no) per possible edge
*/
vector<Kmer> Kmer::_getOutgoingEdges(uint8_t edges,int k){
vector<Kmer> b;
Kmer aTemplate;
aTemplate=*this;
for(int i=0;i<aTemplate.getNumberOfU64();i++){
uint64_t word=aTemplate.getU64(i)>>2;
if(i!=aTemplate.getNumberOfU64()-1){
uint64_t next=aTemplate.getU64(i+1);
/*
* abcd efgh
* 00ab 00ef
* 00ab cdef
*/
next=(next<<62);
word=word|next;
}
aTemplate.setU64(i,word);
}
int positionToUpdate=2*k;
int chunkIdToUpdate=positionToUpdate/64;
positionToUpdate=positionToUpdate%64;
for(int i=0;i<4;i++){
int j=((((uint64_t)edges)<<(sizeof(uint64_t)*8-5-i))>>(sizeof(uint64_t)*8-1));
if(j==1){
Kmer newKmer=aTemplate;
uint64_t last=newKmer.getU64(chunkIdToUpdate);
uint64_t filter=i;
filter=filter<<(positionToUpdate-2);
last=last|filter;
newKmer.setU64(chunkIdToUpdate,last);
b.push_back(newKmer);
}
}
return b;
}
void SpuriousSeedAnnihilator::call_RAY_SLAVE_MODE_REGISTER_SEEDS(){
if(!m_debugCode && m_parameters->hasCheckpoint("Seeds")){
m_hasCheckpointFilesForSeeds = true;
}
if((!m_debugCode && m_hasCheckpointFilesForSeeds) || m_skip){
m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
return;
}
if(m_inbox->hasMessage(RAY_MESSAGE_TAG_PUSH_SEEDS_REPLY)){
m_activeQueries--;
return;
}
#ifdef ASSERT
assert(m_activeQueries>=0);
#endif
if(m_activeQueries > 0)
return;
#ifdef ASSERT
assert(m_activeQueries==0);
#endif
if(m_seedIndex < (int)m_seeds->size()){
if(m_seedPosition < (*m_seeds)[m_seedIndex].size()){
if(m_seedIndex==0 && m_seedPosition == 0)
cout<<"Rank "<<m_core->getRank()<<" has "<<m_seeds->size()<<" seeds to register."<<endl;
Kmer vertex;
(*m_seeds)[m_seedIndex].at(m_seedPosition,&vertex);
Rank destination=m_parameters->vertexRank(&vertex);
MessageTag tag=RAY_MESSAGE_TAG_PUSH_SEEDS;
int elements = m_virtualCommunicator->getElementsPerQuery(tag);
for(int i=0;i<vertex.getNumberOfU64();i++){
m_buffers.addAt(destination,vertex.getU64(i));
}
PathHandle identifier = getPathUniqueId(m_rank, m_seedIndex);
m_buffers.addAt(destination, identifier);
m_buffers.addAt(destination, m_seedPosition);
if(m_buffers.flush(destination, elements, tag, m_outboxAllocator, m_outbox, m_rank,false)){
m_activeQueries++;
}
if(m_seedPosition % 1000 == 0) {
cout << "Rank "<<m_rank << " registered " << m_seedIndex << "/" <<m_seeds->size();
cout<< " "<< m_seedPosition << "/" << (*m_seeds)[m_seedIndex].size() << endl;
}
m_seedPosition++;
}else{
if(m_seedIndex % 100 == 0)
cout << "Rank "<<m_rank << " registered " << m_seedIndex << "/" <<m_seeds->size() << endl;
m_seedIndex++;
m_seedPosition = 0;
}
}else if(!m_buffers.isEmpty()){
/**
* Flush additional queries
*/
MessageTag tag=RAY_MESSAGE_TAG_PUSH_SEEDS;
m_activeQueries += m_buffers.flushAll(tag, m_outboxAllocator, m_outbox, m_rank);
}else{
m_seedIndex=0;
m_seedPosition=0;
cout << "Rank "<<m_rank << " registered " << m_seedIndex - 1 << "/" <<m_seeds->size() << endl;
cout<<"Rank "<<m_rank << " registered its seeds" << endl;
m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
}
}
