void collapseDuplexGroup(string sorted_duplex_group_file, string collapsed_dg_file, string logFile, string errorFile, int maxGap, int maxTotal)
{
ofstream LOG(logFile, ios_base::app);
ofstream ERR(errorFile, ios_base::app);
LOG << "Start to collapseDuplexGroup " << sorted_duplex_group_file << " ===> " << collapsed_dg_file << endl;
int merged_dgCount = 0;
int firstPossible=0;
PointerArray<DuplexGroup *> dgArray;
long long fileLines = countFileLines(sorted_duplex_group_file);
ProcessAlert alert(fileLines, 100000, 10);
ifstream DUPLEXGROUP(sorted_duplex_group_file);
char strand1, strand2;
string chr1, chr2, supportReads;
int start1, end1, start2, end2, support;
while(DUPLEXGROUP>>chr1>>start1>>end1>>strand1>>chr2>>start2>>end2>>strand2>>supportReads>>support)
{
char buffer[200];
sprintf(buffer, "firstPossible: %d, merged_dgCount: %d", firstPossible, merged_dgCount);
LOG << alert.alert(string(buffer));
DuplexGroup *dg = new DuplexGroup(chr1, start1, end1, strand1, chr2, start2,end2, strand2, support, supportReads);
//dgArray.append(dg);
//if(supportReads == "23198;10015265;10015267;10015268")
// cout << dgArray[dgArray.arrayLen()-1]->supportRead << endl;
int lastDGovarlapped = 0; bool merged = false;
for(int idx=firstPossible; idx<dgArray.arrayLen();idx++)
{
int overlapped = dgArray[idx]->overlapDG(dg, maxGap, maxTotal);
/*
if(supportReads == "23198;10015265;10015267;10015268" and idx==dgArray.arrayLen()-1)
{
cout << dgArray[dgArray.arrayLen()-1]->supportRead << endl;
cout <<overlapped << endl;
}
*/
if (overlapped == -1){
if(not lastDGovarlapped)
firstPossible = idx + 1;
}
else if(overlapped > 0){
lastDGovarlapped = 1;
dgArray[idx]->mergeDuplexGroup(dg);
//dgArray.del(dgArray.arrayLen()-1);
merged = true;
delete dg;
merged_dgCount++;
break;
}
else{
lastDGovarlapped = 1;
}
}
if(not merged)
dgArray.append(dg);
//cout << merged_dgCount << endl;
}
LOG << alert.finish();
DUPLEXGROUP.close();
ofstream COLLAPSE(collapsed_dg_file);
for(int i=0; i<dgArray.arrayLen(); i++)
COLLAPSE << dgArray[i]->chr1 << "\t" << dgArray[i]->start1 << "\t" << dgArray[i]->end1 << "\t" << dgArray[i]->strand1 << "\t" << dgArray[i]->chr2 << "\t" << dgArray[i]->start2 << "\t" << dgArray[i]->end2 << "\t" << dgArray[i]->strand2 << "\t" << dgArray[i]->supportRead << "\t" << dgArray[i]->support << "\n";
COLLAPSE.close();
LOG.close();
ERR.close();
}
void genDuplexGroup(string read_pair_file, string duplex_group_file, string logFile, string errorFile, int OVERLAP, bool multiDG)
{
ofstream LOG(logFile, ios_base::app);
ofstream ERR(errorFile, ios_base::app);
LOG << "Start to genDuplexGroup " << read_pair_file << " ===> " << duplex_group_file << endl;
long long fileLines = countFileLines(read_pair_file);
ProcessAlert alert(fileLines, 100000, 10);
ifstream READPAIR(read_pair_file);
char strand1, strand2;
string chr1, chr2;
int start1, end1, id1, score1, start2, end2, id2, score2;
int counter = 0;
int firstPossible = 0;
int dgCount = 0;
PointerArray<DuplexGroup *> dgArray;
while(READPAIR>>chr1>>start1>>end1>>id1>>score1>>strand1>>chr2>>start2>>end2>>id2>>score2>>strand2)
{
char buffer[200];
sprintf(buffer, "firstPossible: %d, duplexCount: %d", firstPossible, dgCount);
LOG << alert.alert(string(buffer));
Read read(chr1, start1, end1, strand1, chr2, start2, end2, strand2, id1);
int nonOverlapped = 1;
int lastDGoverlapped = 0;
for(int i=firstPossible;i<dgCount;i++)
{
int overlap = dgArray[i]->overlapRead(read);
//cout << overlap << endl;
if(overlap >= OVERLAP)
{
lastDGoverlapped = 1;
nonOverlapped = 0;
dgArray[i]->addRead(read);
//cout << "find one" << endl;
if (! multiDG) break;
}else if (overlap == -1){
if(not lastDGoverlapped)
firstPossible = i + 1;
}else
{
lastDGoverlapped = 1;
}
}
if (nonOverlapped)
{
DuplexGroup *dg = new DuplexGroup(read);
dgArray.append( dg );
dgCount++;
}
counter++;
}
LOG << alert.finish();
READPAIR.close();
ofstream DUPLEXGROUP(duplex_group_file);
for(int i=0; i<dgArray.arrayLen(); i++)
DUPLEXGROUP << dgArray[i]->chr1 << "\t" << dgArray[i]->start1 << "\t" << dgArray[i]->end1 << "\t" << dgArray[i]->strand1 << "\t" << dgArray[i]->chr2 << "\t" << dgArray[i]->start2 << "\t" << dgArray[i]->end2 << "\t" << dgArray[i]->strand2 << "\t" << dgArray[i]->supportRead << "\t" << dgArray[i]->support << endl;
DUPLEXGROUP.close();
LOG.close();
ERR.close();
}