/* 'ReadBuffer::flush' writes the current contents of the buffer to the
designated output file, and then clears the contents to be ready to receive
the next reads. */
void ReadBuffer::flush()
{
// std::cout << "in flush " << std::endl;
#pragma omp parallel for
for (int i=0; i<m_currentsize ; i++ ) {
// std::cout << "before GetCloseEnd " << std::endl;
GetCloseEnd(m_CHROMOSOME, m_rawreads[i]);
// std::cout << "after GetCloseEnd " << std::endl;
if (m_rawreads[i].hasCloseEnd()) {
//if (m_rawreads[i].Name == "@DD7DT8Q1:4:1106:17724:13906#GTACCT/1") {
// std::cout << "m_rawreads[i].hasCloseEnd()" << std::endl;
//}
updateReadAfterCloseEndMapping(m_rawreads[i]);
#pragma omp critical
m_filteredReads.push_back(m_rawreads[i]);
}
else {
//if (m_rawreads[i].Name == "@DD7DT8Q1:4:1106:17724:13906#GTACCT/1") {
// std::cout << "m_rawreads[i] no close end" << std::endl;
//}
#pragma omp critical
m_OneEndMappedReads.push_back(m_rawreads[i]);
}
}
//std::cout << "end of flush " << std::endl;
m_rawreads.clear();
m_currentsize = 0;
//std::cout << "existing flush " << std::endl;
}
/* 'ReadBuffer::flush' writes the current contents of the buffer to the
designated output file, and then clears the contents to be ready to receive
the next reads. */
void ReadBuffer::flush()
{
// std::cout << "in flush " << std::endl;
#pragma omp parallel for
for (int i=0; i<m_currentsize ; i++ ) {
// std::cout << "before GetCloseEnd " << std::endl;
//std::map<std::string, unsigned>::iterator it = g_ReadSeq2Index.find(m_rawreads[i].UnmatchedSeq);
//if (it == g_ReadSeq2Index.end())
{
//if (m_rawreads[i].MapperSplit ) {
// std::cout << "skip close end search" << std::endl;
//}
if (m_rawreads[i].MapperSplit == false)
GetCloseEnd(m_CHROMOSOME, m_rawreads[i]);
if (m_rawreads[i].hasCloseEnd()) {
updateReadAfterCloseEndMapping(m_rawreads[i]);
#pragma omp critical
{
// g_ReadSeq2Index.insert(std::pair<std::string, unsigned> (m_rawreads[i].UnmatchedSeq, m_filteredReads.size()));
m_rawreads[i].SampleName2Number.insert(std::pair <std::string, unsigned> (m_rawreads[i].Tag, 1));
m_filteredReads.push_back(m_rawreads[i]);
}
}
// else {
//if (m_rawreads[i].Name == "@DD7DT8Q1:4:1106:17724:13906#GTACCT/1") {
// std::cout << "m_rawreads[i] no close end" << std::endl;
//}
//#pragma omp critical
//m_OneEndMappedReads.push_back(m_rawreads[i]);
// }
}
//else { // SampleName2Number std::map <std::string, unsigned> SampleName2Number;
// #pragma omp critical
// {
// unsigned ReadIndex = it -> second; // m_filteredReads[ReadIndex]
// std::map <std::string, unsigned>::iterator it_SampleName = m_filteredReads[ReadIndex].SampleName2Number.find(m_rawreads[i].Tag);
//
// if (it_SampleName == m_filteredReads[ReadIndex].SampleName2Number.end()) {
// //std::cout << "adding " << m_rawreads[i].Tag << "\t1" << std::endl;
// m_filteredReads[ReadIndex].SampleName2Number.insert(std::pair <std::string, unsigned> (m_rawreads[i].Tag, 1));
// }
// else {
//
// it_SampleName -> second++;
// //std::cout << "increasing " << m_rawreads[i].Tag << "\t" << it_SampleName -> second << std::endl;
// }
// }
//}
// std::cout << "after GetCloseEnd " << std::endl;
}
//std::cout << "end of flush " << std::endl;
m_rawreads.clear();
m_currentsize = 0;
//std::cout << "existing flush " << std::endl;
}
