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AmpliconClipper.cpp
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AmpliconClipper.cpp
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#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <algorithm>
#include <vector>
#include <climits>
#include <stdlib.h>
#include <cstring>
#include <stdint.h>
#include "options.hpp"
#include "read.hpp"
#include "amplicon.hpp"
std::vector<std::string> header_strings;
std::vector<std::read> read_container;
std::amplicons_list Amplicons;
std::amplicon_strands forwardAmplicons;
std::amplicon_strands reverseAmplicons;
void processReadWithAmplicon(const std::amplicon& Amplicon, std::read& Read)
{
int curPos, toCut, overshoot, start, cLength = 0;
char cCigar;
std::stringstream newCIGAR;
// set discard flag for unwanted amplicons
if ((std::min(Read.EndPOS, Amplicon.insertEnd) - std::max(Read.POS, Amplicon.insertStart) <= 0) || (Amplicon.discardReads))
{
// read lies wholely within primer
Read.keep = false;
}
else
{
// trim the lower end
if (std::min(Read.EndPOS, Amplicon.insertStart) - std::max(Read.POS, Amplicon.ampliconStart) > 0)
{
// there is overlap with the 5' PCR primer
curPos = Read.POS;
toCut = 0;
start = 0;
cCigar = '-';
int i = 0;
while ((curPos <= Amplicon.insertStart) || (cCigar != 'M'))
{
cLength = 0;
while (isdigit(cCigar = Read.CIGAR.at(++i)));
cLength = atoi(Read.CIGAR.substr(start, i - start).c_str());
if (cCigar != 'I')
{
curPos += cLength;
}
if (cCigar != 'D')
{
toCut += cLength;
}
start = i+1;
}
overshoot = (curPos - Amplicon.insertStart);
int startOffset = (overshoot >= cLength ? cLength : overshoot);
toCut -= startOffset;
newCIGAR.clear();
newCIGAR.str(std::string());
newCIGAR << startOffset << cCigar << Read.CIGAR.substr(start);
/*
// C++11:
newCIGAR = std::to_string(startOffset);
newCIGAR += cCigar;
newCIGAR.append(Read.CIGAR.substr(start));
*/
Read.CIGAR = newCIGAR.str();
Read.POS = curPos - startOffset;
Read.SEQ.erase(0, toCut);
if (Read.QUAL != "*")
Read.QUAL.erase(0, toCut);
}
// trim upper end
std::string tempCigar;
if (std::min(Read.EndPOS, Amplicon.ampliconEnd) - std::max(Read.POS, Amplicon.insertEnd) > 0)
{
// there is overlap with the 3' PCR primer
curPos = Read.EndPOS;
tempCigar = 'M' + Read.CIGAR;
toCut = 0;
start = tempCigar.length() - 1;
cCigar = tempCigar.at(start);
int i = tempCigar.length() - 2;
while ((curPos >= Amplicon.insertEnd) || (cCigar != 'M'))
{
cCigar = tempCigar.at(start);
cLength = 0;
while (isdigit(tempCigar.at(--i)));
cLength = atoi(tempCigar.substr(i+1, i+1 - start).c_str());
if (cCigar != 'I')
{
curPos -= cLength;
}
if (cCigar != 'D')
{
toCut += cLength;
}
start = i;
--i;
}
overshoot = (Amplicon.insertEnd - curPos);
int endOffset = (overshoot >= cLength ? cLength : overshoot);
toCut -= endOffset;
newCIGAR.clear();
newCIGAR.str(std::string());
newCIGAR << tempCigar.substr(1, start) << endOffset << cCigar;
/*
// C++11:
newCIGAR = tempCigar.substr(1, start);
newCIGAR.append(std::to_string(endOffset));
newCIGAR += cCigar;
*/
Read.EndPOS = curPos + endOffset;
Read.CIGAR = newCIGAR.str();
Read.SEQ.erase(Read.SEQ.length()-toCut, std::string::npos);
if (Read.QUAL != "*")
Read.QUAL.erase(Read.QUAL.length()-toCut, std::string::npos);
}
}
Read.calculateLengthOnGenome();
assert(Read.EndPOS - Read.POS == Read.LengthOnGenome);
if (static_cast<double>(std::min(Read.EndPOS, Amplicon.insertEnd) - std::max(Read.POS, Amplicon.insertStart))/(Amplicon.insertEnd - Amplicon.insertStart) < min_amplicon_coverage)
{
// is too short for amplicon
Read.keep = false;
}
//else
// std::cout << Read.QNAME << " : " << std::min(Read.EndPOS, Amplicon.insertEnd) - std::max(Read.POS, Amplicon.insertStart) << " : " << static_cast<double>(std::min(Read.EndPOS, Amplicon.insertEnd) - std::max(Read.POS, Amplicon.insertStart))/(Amplicon.insertEnd - Amplicon.insertStart) << "\n";
}
int main(int argc, char** argv)
{
parse_arguments(argc, argv);
std::string line;
if (!(amplicon_input.empty()))
{
// read amplicon input file
read_amplicon_input(amplicon_input, Amplicons, forwardAmplicons, reverseAmplicons);
}
// read SAM input file
std::ifstream sam_input_File(sam_input.c_str());
if (sam_input_File.is_open())
{
// Retrieve the header, store it in vector header_strings;
getline(sam_input_File, line);
while (line[0] == '@')
{
line.erase(std::remove(line.begin(), line.end(), '\n'), line.end());
header_strings.push_back(line);
getline(sam_input_File, line);
}
do
{
line.erase(std::remove(line.begin(), line.end(), '\n'), line.end());
read_container.push_back(std::read(line));
}
while (getline(sam_input_File, line));
}
else
{
std::cout << "The input file '" << sam_input << "' does not exist.\n";
return 1;
}
sam_input_File.close();
// Perform actual trimming
std::amplicon_strands::const_iterator iter_start, iter_end, best_amplicon;
int overlap, max_overlap = 0;
for (uint32_t i = 0; i < read_container.size(); ++i)
{
read_container[i].clipNBasesFromFront(n_BasesFront);
read_container[i].clipNBasesFromBack(n_BasesBack);
if (read_container[i].CigarI > max_insertions)
read_container[i].keep = false;
if (read_container[i].CigarD > max_deletions)
read_container[i].keep = false;
if (read_container[i].maxContigDel > max_cont_deletion)
read_container[i].keep = false;
if (!(amplicon_input.empty()))
{
if (read_container[i].isReverse)
{
// reverse strand read
iter_start = reverseAmplicons.begin();
iter_end = reverseAmplicons.end();
}
else
{
// forward strand read
iter_start = forwardAmplicons.begin();
iter_end = forwardAmplicons.end();
}
// choose the best amplicon based on overlap
max_overlap = 0;
overlap = 0;
for (std::amplicon_strands::const_iterator j = iter_start; j != iter_end; ++j)
{
overlap = (*j)->readOverlap(read_container[i]);
if (overlap > max_overlap)
{
max_overlap = overlap;
best_amplicon = j;
}
}
if (max_overlap > 0)
{
processReadWithAmplicon(*(*best_amplicon), read_container[i]);
read_container[i].calculateLengthOnGenome();
}
else
{
read_container[i].keep = false;
}
}
}
// write final SAM output
std::ofstream sam_output_File(sam_output.c_str());
if (sam_output_File.is_open())
{
// header:
for (uint32_t i = 0; i < header_strings.size(); ++i)
{
sam_output_File << header_strings[i] << '\n';
}
for (uint32_t i = 0; i < read_container.size(); ++i)
{
if (read_container[i].keep)
sam_output_File << read_container[i] << '\n';
}
}
sam_output_File.close();
// write statistics
if (write_statistics)
{
std::ofstream stats_output_File("stats.txt");
stats_output_File << "M\tI\tD\n";
for (uint32_t i = 0; i < read_container.size(); ++i)
{
if (read_container[i].keep)
stats_output_File << read_container[i].CigarM << '\t' << read_container[i].CigarI << '\t' << read_container[i].CigarD << '\n';
}
stats_output_File.close();
}
return 0;
}