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controlLayer4.cpp
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/*
* =====================================================================================
*
* Filename: controlLayer.cpp
*
* Description:
*
* Version: 1.0
* Created: 06/25/2017 09:38:26
* Revision: none
* Compiler: gcc
*
* Author: Baoxing Song (songbx.me), songbaoxing168@163.com
*
* =====================================================================================
*/
/*************************************************************************
************************************************************************/
#include "controlLayer.h"
std::string softwareName = "dCNS";
int32_t seed_window_size = 38;
int32_t mini_cns_score = 40;
int32_t step_size = 8;
int32_t matrix_boundary_distance = 0;
int32_t matchingScore = 2;
int32_t mismatchingPenalty = -3;
int32_t openGapPenalty1 = -4;
int32_t extendGapPenalty1 = -2;
int32_t openGapPenalty2 = -45;
int32_t extendGapPenalty2 = 0;
int32_t zDrop = 50; // this one should be slightly larger than openGapPenalty2
int32_t bandwidth = 20000; // using very large value
double lambda = 0.382291; // for 100kb *100kb sequence alignment, score 53-54 gives a p-value around 0.1
double kValue = 0.006662;
bool onlySyntenic = false;
double pvalues = 0.1;
int32_t w = 10; //this is the band width for band sequence alignments
int32_t xDrop = 20;
void outputNoMasking(std::string _output, std::vector<PairedSimilarFragment> pairedSimilarFragments0, int32_t refStrand,
int32_t queStrand, int32_t refStart, int32_t queStart, std::string refChr, std::string queChr,
std::string & seq1_string, std::string & seq2_string){
std::ofstream ofile;
ofile.open(_output+".sam", std::ios_base::app);
std::ofstream ofile2;
ofile2.open(_output+"o", std::ios_base::app);
// std::cout << "line 63, size:" << pairedSimilarFragments0.size() <<"refStrand:" << refStrand << "queStrand:" << queStrand<< std::endl;
// ofile << "@SQ\tSN:8\tLN:181122637" << std::endl;
ofile2 << "#" << refChr << ":" << refStrand << ":" << refStart << "-" << queChr << ":" << queStrand << ":" << queStart << std::endl;
for( int32_t i=0; i<pairedSimilarFragments0.size(); ++i ){
if( refStrand == 1 && 1==queStrand ){
int32_t quePos = queStart + pairedSimilarFragments0[i].getStart2() - 1;
int32_t refPos = refStart + pairedSimilarFragments0[i].getStart1() - 1;
ofile << queChr << "\t0\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragments0[i].getScore() << "\t" << quePos << "H";
for( int32_t j=0; j<pairedSimilarFragments0[i].getCigar().size(); ++j ){
uint32_t cigarLength = pairedSimilarFragments0[i].getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragments0[i].getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragments0[i].getStart2(), pairedSimilarFragments0[i].getEnd2()) << "\t*" << std::endl;
}else if ( refStrand == 0 && 1==queStrand){
int32_t quePos = queStart + pairedSimilarFragments0[i].getStart2() - 1;
int32_t refPos = refStart + seq1_string.size() -1 - pairedSimilarFragments0[i].getEnd1()+1;
ofile << queChr << "\t16\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragments0[i].getScore() << "\t" << quePos << "H";
for( int32_t j=pairedSimilarFragments0[i].getCigar().size()-1; j>=0; --j ){
uint32_t cigarLength = pairedSimilarFragments0[i].getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragments0[i].getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragments0[i].getStart2(), pairedSimilarFragments0[i].getEnd2(), 0) << "\t*" << std::endl;
}else if( refStrand == 1 && 0==queStrand ){
// std::cout << "line 86" << std::endl;
int32_t quePos = queStart + seq2_string.size()-1-pairedSimilarFragments0[i].getEnd2()+1; // this is the position on the positive strand
int32_t refPos = refStart + pairedSimilarFragments0[i].getStart1() - 1;
ofile << queChr << "\t16\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragments0[i].getScore() << "\t" << quePos << "H";
for( int32_t j=0; j<pairedSimilarFragments0[i].getCigar().size(); ++j ){
uint32_t cigarLength = pairedSimilarFragments0[i].getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragments0[i].getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragments0[i].getStart2(), pairedSimilarFragments0[i].getEnd2()) << "\t*" << std::endl;
}else if( refStrand == 0 && refStrand==queStrand ){
int32_t quePos = queStart + seq2_string.size()-1-pairedSimilarFragments0[i].getEnd2()+1;
int32_t refPos = refStart + seq1_string.size() -1 - pairedSimilarFragments0[i].getEnd1()+1;
ofile << queChr << "\t0\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragments0[i].getScore() << "\t" << quePos << "H";
for( int32_t j=pairedSimilarFragments0[i].getCigar().size()-1; j>=0; --j ){
uint32_t cigarLength = pairedSimilarFragments0[i].getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragments0[i].getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragments0[i].getStart2(), pairedSimilarFragments0[i].getEnd2(), 0) << "\t*" << std::endl;
}
ofile2 << pairedSimilarFragments0[i].getStart1() << " " << pairedSimilarFragments0[i].getEnd1()
<< " " << pairedSimilarFragments0[i].getStart2() << " " << pairedSimilarFragments0[i].getEnd2() << " " << pairedSimilarFragments0[i].getScore() << " " << pairedSimilarFragments0[i].getPValue() << std::endl;
}
ofile.close();
ofile2 << "#done" << std::endl;
ofile2.close();
}
void outputNoMasking(std::string _output, PairedSimilarFragment pairedSimilarFragment, int32_t refStrand,
int32_t queStrand, int32_t refStart, int32_t queStart, std::string refChr, std::string queChr,
std::string & seq1_string, std::string & seq2_string){
std::ofstream ofile;
ofile.open(_output+".sam", std::ios_base::app);
std::ofstream ofile2;
ofile2.open(_output+"o", std::ios_base::app);
ofile2 << "#" << refChr << ":" << refStrand << ":" << refStart << "-" << queChr << ":" << queStrand << ":" << queStart << std::endl;
if( refStrand == 1 && 1==queStrand ){
int32_t quePos = queStart + pairedSimilarFragment.getStart2() - 1;
int32_t refPos = refStart + pairedSimilarFragment.getStart1() - 1;
ofile << queChr << "\t0\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragment.getScore() << "\t" << quePos << "H";
for( int32_t j=0; j<pairedSimilarFragment.getCigar().size(); ++j ){
uint32_t cigarLength = pairedSimilarFragment.getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragment.getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragment.getStart2(), pairedSimilarFragment.getEnd2()) << "\t*" << std::endl;
}else if ( refStrand == 0 && 1==queStrand){
int32_t quePos = queStart + pairedSimilarFragment.getStart2() - 1;
int32_t refPos = refStart + seq1_string.size() -1 - pairedSimilarFragment.getEnd1()+1;
ofile << queChr << "\t16\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragment.getScore() << "\t" << quePos << "H";
for( int32_t j=pairedSimilarFragment.getCigar().size()-1; j>=0; --j ){
uint32_t cigarLength = pairedSimilarFragment.getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragment.getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragment.getStart2(), pairedSimilarFragment.getEnd2(), 0) << "\t*" << std::endl;
}else if( refStrand == 1 && 0==queStrand ){
// std::cout << "line 86" << std::endl;
int32_t quePos = queStart + seq2_string.size()-1-pairedSimilarFragment.getEnd2()+1; // this is the position on the positive strand
int32_t refPos = refStart + pairedSimilarFragment.getStart1() - 1;
ofile << queChr << "\t16\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragment.getScore() << "\t" << quePos << "H";
for( int32_t j=0; j<pairedSimilarFragment.getCigar().size(); ++j ){
uint32_t cigarLength = pairedSimilarFragment.getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragment.getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragment.getStart2(), pairedSimilarFragment.getEnd2()) << "\t*" << std::endl;
}else if( refStrand == 0 && refStrand==queStrand ){
int32_t quePos = queStart + seq2_string.size()-1-pairedSimilarFragment.getEnd2()+1;
int32_t refPos = refStart + seq1_string.size() -1 - pairedSimilarFragment.getEnd1()+1;
ofile << queChr << "\t0\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragment.getScore() << "\t" << quePos << "H";
for( int32_t j=pairedSimilarFragment.getCigar().size()-1; j>=0; --j ){
uint32_t cigarLength = pairedSimilarFragment.getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragment.getCigar()[j]&0xf;
ofile << cigarLength << "MID"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_string, pairedSimilarFragment.getStart2(), pairedSimilarFragment.getEnd2(), 0) << "\t*" << std::endl;
}
ofile2 << pairedSimilarFragment.getStart1() << " " << pairedSimilarFragment.getEnd1()
<< " " << pairedSimilarFragment.getStart2() << " " << pairedSimilarFragment.getEnd2() << " " << pairedSimilarFragment.getScore() << " " << pairedSimilarFragment.getPValue() << std::endl;
ofile.close();
ofile2 << "#done" << std::endl;
ofile2.close();
}
void pairCnsXExtend(std::string & _input, std::string & _reference, std::string & _output,
int32_t & _matchingScore, int32_t & _mismatchingPenalty, int32_t & _openGapPenalty,
int32_t & _extendGapPenalty, int32_t & _seed_window_size, int32_t & _mini_cns_score,
int32_t & _step_size, int32_t & _matrix_boundary_distance, bool & _onlySyntenic, const double & _lambda,
const double & _kValue, const int32_t & _w, const int32_t & _xDrop, double & _pvalues){
Scorei m(_matchingScore, _mismatchingPenalty);
std::map<std::string, std::string> sequences;
std::vector<std::string> seqNames;
std::map<std::string, FastaMeta> metaInformations;
readFastaFile( _input, sequences, metaInformations, seqNames );
SequenceCharToUInt8 sequenceCharToUInt8;
std::string seq1_string = sequences[_reference];
int8_t * seq1 = sequenceCharToUInt8.seq_to_int8(seq1_string);
int8_t * seq1_rev_com = sequenceCharToUInt8.rev_comp(seq1, seq1_string.length());
int32_t length1 = seq1_string.length();
//sequences.clear();
std::cout << "reference:" << seq1_string << std::endl;
for( std::string _query : seqNames ){
if( _query.compare(_reference) != 0) {
std::string seq2_string = sequences[_query];
//seq2_string = getReverseComplementary(seq2_string);
int8_t *seq2 = sequenceCharToUInt8.seq_to_int8(seq2_string);
int8_t *seq2_rev_com = sequenceCharToUInt8.rev_comp(seq2, seq2_string.length());
int32_t length2 = seq2_string.length();
std::cout << "_query:" << _query << ": " << seq2_string << std::endl;
std::vector<PairedSimilarFragment> pairedSimilarFragments0 =
findSimilarFragmentsForPairedSequence(seq1, seq1_rev_com,
seq2, seq2_rev_com, length1, length2, _seed_window_size,
_mini_cns_score, _matrix_boundary_distance, _openGapPenalty,
_extendGapPenalty, _matchingScore,
_mismatchingPenalty, m, _step_size, seq1_string, seq2_string,
_pvalues, _lambda, _kValue, _w, _xDrop);
if (_onlySyntenic) {
std::vector<PairedSimilarFragment> pairedSimilarFragments = syntenic(pairedSimilarFragments0);
pairedSimilarFragments0 = pairedSimilarFragments;
}
outputNoMasking(_output+metaInformations[_query].getSpecies(), pairedSimilarFragments0,
metaInformations[_reference].getStrand(), metaInformations[_query].getStrand(),
metaInformations[_reference].getStart(), metaInformations[_query].getStart(),
metaInformations[_reference].getChr(), metaInformations[_query].getChr(),
seq1_string, seq2_string);
delete seq2;
delete seq2_rev_com;
}
}
delete seq1;
delete seq1_rev_com;
}
int pairCnsXExtend(int argc, char** argv){
std::stringstream usage;
usage << "Usage: "<<softwareName<<" pairCnsXExtend -i input -r reference -q query -o output" << std::endl<<
"Options" << std::endl <<
" -i FILE input file in fasta format" << std::endl <<
" -r STRING reference sequence entry name in input fasta file" << std::endl <<
// " -q STRING query sequence entry name in input fasta file" << std::endl <<
" -o FILE output file, exists file will be overwrote" << std::endl <<
" -y bool only output syntenic result (default: false)" << std::endl <<
" -A INT Matching score (default: " << matchingScore << ")" << std::endl <<
" -B INT Mismatching penalty (default: " << mismatchingPenalty << ")" << std::endl <<
" -O INT open gap penalty (default: " << openGapPenalty1 << ")" << std::endl <<
" -E INT extend gap penalty (default: " << extendGapPenalty1 << ")" << std::endl <<
" -u INT xextend alignment band width (default: " << w << ")" << std::endl <<
" -w INT the windows size used to run the smith-waterman algorithm to get the alignment seed (default: "<<seed_window_size<<")" << std::endl <<
//" -m INT minimum seeds size to trigger a alignment extension and the minimum conserved sequence to report (default: " << mini_cns_seed_size << ")" << std::endl <<
" -c INT minimum seeds score to trigger a alignment extension (default: " << mini_cns_score << ")" << std::endl <<
" -s INT step size for sliding the smith-waterman seeds alignment window (default: " << step_size << ")" << std::endl <<
" -l DOUBLE lambda value for pvalue caculation (default: " << lambda << ")" << std::endl <<
" -k DOUBLE k value for pvalue caculation (default: " << kValue << ")" << std::endl <<
" -p DOUBLE pvalue for significant alignment output (default: " << pvalues << ")" << std::endl <<
" -b INT minimum number of base-pairs between the maximum smith-waterman score with the score matrix boundary (default: " << matrix_boundary_distance << ") , it is not important" << std::endl;
InputParser inputParser (argc, argv);
if( inputParser.cmdOptionExists("-A") ){
matchingScore = std::stoi( inputParser.getCmdOption("-A") );
}
if( inputParser.cmdOptionExists("-B") ){
mismatchingPenalty = std::stoi( inputParser.getCmdOption("-B") );
}
if( inputParser.cmdOptionExists("-O") ){
openGapPenalty1 = std::stoi( inputParser.getCmdOption("-O") );
}
if( inputParser.cmdOptionExists("-E") ){
extendGapPenalty1 = std::stoi( inputParser.getCmdOption("-E") );
}
if( inputParser.cmdOptionExists("-u") ){
w = std::stoi( inputParser.getCmdOption("-u") );
}
if( inputParser.cmdOptionExists("-y") ){
onlySyntenic = str2bool( inputParser.getCmdOption("-y"), onlySyntenic );
}
if( inputParser.cmdOptionExists("-w") ){
seed_window_size = std::stoi( inputParser.getCmdOption("-w") );
}
if( inputParser.cmdOptionExists("-c") ){
mini_cns_score = std::stoi( inputParser.getCmdOption("-c") );
}
if( inputParser.cmdOptionExists("-s") ){
step_size = std::stoi( inputParser.getCmdOption("-s") );
}
if( inputParser.cmdOptionExists("-b") ){
matrix_boundary_distance = std::stoi( inputParser.getCmdOption("-b") );
}
if( inputParser.cmdOptionExists("-l") ){
lambda = std::stod( inputParser.getCmdOption("-l") );
}
if( inputParser.cmdOptionExists("-k") ){
kValue = std::stod( inputParser.getCmdOption("-k") );
}
if( inputParser.cmdOptionExists("-p") ){
pvalues = std::stod( inputParser.getCmdOption("-p") );
}
if(inputParser.cmdOptionExists("-h") ||inputParser.cmdOptionExists("--help") ){
std::cerr << usage.str();
}else if( inputParser.cmdOptionExists("-i") && inputParser.cmdOptionExists("-r") && /*inputParser.cmdOptionExists("-q") &&*/ inputParser.cmdOptionExists("-o") ){
std::string input = inputParser.getCmdOption("-i");
std::string reference = inputParser.getCmdOption("-r");
//std::string query = inputParser.getCmdOption("-q");
std::string output = inputParser.getCmdOption("-o");
pairCnsXExtend(input, reference, output, matchingScore, mismatchingPenalty, openGapPenalty1,
extendGapPenalty1, seed_window_size, mini_cns_score,
step_size, matrix_boundary_distance, onlySyntenic, lambda, kValue, w, xDrop, pvalues);
return 0;
}else{
std::cerr << usage.str();
}
return 1;
}
void pairCns2Gaps(std::string & _input, std::string & _reference, std::string & _output,
int32_t & _matchingScore, int32_t & _mismatchingPenalty, int32_t & _openGapPenalty1,
int32_t & _extendGapPenalty1, int32_t & _openGapPenalty2,
int32_t & _extendGapPenalty2, int32_t & _seed_window_size, int32_t & _mini_cns_score,
int32_t & _step_size, int32_t & _matrix_boundary_distance, bool & _onlySyntenic, const double & _lambda,
const double & _kValue, const int32_t & _w, const int32_t & _bandwidth, const int32_t & _xDrop,
const int32_t & _zDrop, double & _pvalues){
std::map<std::string, FastaMeta> metaInformations;
Scorei m(_matchingScore, _mismatchingPenalty);
std::map<std::string, std::string> sequences;
std::vector<std::string> seqNames;
readFastaFile( _input, sequences, metaInformations, seqNames );
SequenceCharToUInt8 sequenceCharToUInt8;
std::string seq1_string = sequences[_reference];
int8_t * seq1 = sequenceCharToUInt8.seq_to_int8(seq1_string);
int8_t * seq1_rev_com = sequenceCharToUInt8.rev_comp(seq1, seq1_string.length());
int32_t length1 = seq1_string.length();
sequences.clear();
for( std::string _query : seqNames ){
if( _query.compare(_reference) != 0) {
std::string seq2_string = sequences[_query];
int8_t *seq2 = sequenceCharToUInt8.seq_to_int8(seq2_string);
int8_t *seq2_rev_com = sequenceCharToUInt8.rev_comp(seq2, seq2_string.length());
int32_t length2 = seq2_string.length();
std::vector<PairedSimilarFragment> pairedSimilarFragments0 =
findSimilarFragmentsForPairedSequence (seq1, seq1_rev_com, seq2, seq2_rev_com, length1, length2,
_seed_window_size, _mini_cns_score,
_matrix_boundary_distance, _openGapPenalty1, _extendGapPenalty1,
_openGapPenalty2, _extendGapPenalty2, _matchingScore,
_mismatchingPenalty, m, _step_size, seq1_string, seq2_string, _pvalues,
_lambda, _kValue, _zDrop, _bandwidth, _w, _xDrop);
if (_onlySyntenic) {
std::vector<PairedSimilarFragment> pairedSimilarFragments = syntenic(pairedSimilarFragments0);
pairedSimilarFragments0 = pairedSimilarFragments;
}
outputNoMasking(_output+metaInformations[_query].getSpecies(), pairedSimilarFragments0, metaInformations[_reference].getStrand(),
metaInformations[_query].getStrand(), metaInformations[_reference].getStart(), metaInformations[_query].getStart(), metaInformations[_reference].getChr(), metaInformations[_query].getChr(),
seq1_string, seq2_string);
delete seq2;
delete seq2_rev_com;
}
}
delete seq1;
delete seq1_rev_com;
}
int pairCns2Gaps(int argc, char** argv){
std::stringstream usage;
usage << "Usage: "<<softwareName<<" pairCns2Gaps -i input -r reference -q query -o output" << std::endl<<
"Options" << std::endl <<
" -i FILE input file in fasta format" << std::endl <<
" -r STRING reference sequence entry name in input fasta file" << std::endl <<
// " -q STRING query sequence entry name in input fasta file" << std::endl <<
" -o FILE output file, exists file will be overwrote" << std::endl <<
" -y bool only output syntenic result (default: false)" << std::endl <<
" -A INT Matching score (default: " << matchingScore << ")" << std::endl <<
" -B INT Mismatching penalty (default: " << mismatchingPenalty << ")" << std::endl <<
" -O1 INT open gap penalty (default: " << openGapPenalty1 << ")" << std::endl <<
" -E1 INT extend gap penalty (default: " << extendGapPenalty1 << ")" << std::endl <<
" -u INT xextend alignment band width (default: " << w << ")" << std::endl <<
" -O2 INT open gap penalty (default: " << openGapPenalty2 << ")" << std::endl <<
" -E2 INT extend gap penalty (default: " << extendGapPenalty2 << ")" << std::endl <<
" -u2 INT z drop alignment band width (default: " << bandwidth << ")" << std::endl <<
//" - INT xextend alignment band width (default: " << extendGapPenalty1 << ")" << std::endl <<
" -w INT the windows size used to run the smith-waterman algorithm to get the alignment seed (default: "<<seed_window_size<<")" << std::endl <<
//" -m INT minimum seeds size to trigger a alignment extension and the minimum conserved sequence to report (default: " << mini_cns_seed_size << ")" << std::endl <<
" -c INT minimum seeds score to trigger a alignment extension (default: " << mini_cns_score << ")" << std::endl <<
" -s INT step size for sliding the smith-waterman seeds alignment window (default: " << step_size << ")" << std::endl <<
" -l DOUBLE lambda value for pvalue caculation (default: " << lambda << ")" << std::endl <<
" -k DOUBLE k value for pvalue caculation (default: " << kValue << ")" << std::endl <<
" -p DOUBLE pvalue for significant alignment output (default: " << pvalues << ")" << std::endl <<
" -b INT minimum number of base-pairs between the maximum smith-waterman score with the score matrix boundary (default: " << matrix_boundary_distance << ") , it is not important" << std::endl;
InputParser inputParser (argc, argv);
if( inputParser.cmdOptionExists("-A") ){
matchingScore = std::stoi( inputParser.getCmdOption("-A") );
}
if( inputParser.cmdOptionExists("-B") ){
mismatchingPenalty = std::stoi( inputParser.getCmdOption("-B") );
}
if( inputParser.cmdOptionExists("-O1") ){
openGapPenalty1 = std::stoi( inputParser.getCmdOption("-O1") );
}
if( inputParser.cmdOptionExists("-E1") ){
extendGapPenalty1 = std::stoi( inputParser.getCmdOption("-E1") );
}
if( inputParser.cmdOptionExists("-O2") ){
openGapPenalty2 = std::stoi( inputParser.getCmdOption("-O2") );
}
if( inputParser.cmdOptionExists("-E2") ){
extendGapPenalty2 = std::stoi( inputParser.getCmdOption("-E2") );
}
if( inputParser.cmdOptionExists("-u") ){
w = std::stoi( inputParser.getCmdOption("-u") );
}
if( inputParser.cmdOptionExists("-u2") ){
bandwidth = std::stoi( inputParser.getCmdOption("-u2") );
}
if( inputParser.cmdOptionExists("-y") ){
onlySyntenic = str2bool( inputParser.getCmdOption("-y"), onlySyntenic );
}
if( inputParser.cmdOptionExists("-w") ){
seed_window_size = std::stoi( inputParser.getCmdOption("-w") );
}
// if( inputParser.cmdOptionExists("-m") ){
// mini_cns_seed_size = std::stoi( inputParser.getCmdOption("-m") );
// }
if( inputParser.cmdOptionExists("-c") ){
mini_cns_score = std::stoi( inputParser.getCmdOption("-c") );
}
if( inputParser.cmdOptionExists("-s") ){
step_size = std::stoi( inputParser.getCmdOption("-s") );
}
if( inputParser.cmdOptionExists("-b") ){
matrix_boundary_distance = std::stoi( inputParser.getCmdOption("-b") );
}
if( inputParser.cmdOptionExists("-l") ){
lambda = std::stod( inputParser.getCmdOption("-l") );
}
if( inputParser.cmdOptionExists("-k") ){
kValue = std::stod( inputParser.getCmdOption("-k") );
}
if( inputParser.cmdOptionExists("-p") ){
pvalues = std::stod( inputParser.getCmdOption("-p") );
}
if(inputParser.cmdOptionExists("-h") ||inputParser.cmdOptionExists("--help") ){
std::cerr << usage.str();
}else if( inputParser.cmdOptionExists("-i") && inputParser.cmdOptionExists("-r") && /*inputParser.cmdOptionExists("-q") &&*/ inputParser.cmdOptionExists("-o") ){
std::string input = inputParser.getCmdOption("-i");
std::string reference = inputParser.getCmdOption("-r");
//std::string query = inputParser.getCmdOption("-q");
std::string output = inputParser.getCmdOption("-o");
pairCns2Gaps(input, reference, output, matchingScore, mismatchingPenalty, openGapPenalty1,
extendGapPenalty1, openGapPenalty2, extendGapPenalty2, seed_window_size, mini_cns_score,
step_size, matrix_boundary_distance, onlySyntenic, lambda, kValue, w, bandwidth, xDrop, zDrop, pvalues);
return 0;
}else{
std::cerr << usage.str();
}
return 1;
}
void weighted1Gap(std::string & _input, std::string & _reference, std::string & _output,
int32_t & _matchingScore, int32_t & _mismatchingPenalty, int32_t & _openGapPenalty1,
int32_t & _extendGapPenalty1, int32_t & _seed_window_size, int32_t & _mini_cns_score,
int32_t & _step_size, int32_t & _matrix_boundary_distance, bool & _onlySyntenic, const double & _lambda,
const double & _kValue, int32_t & _bandwidth, int32_t & _w, const int32_t & _xDrop, const int32_t & _zDrop, const std::string & scoreFoler,
const std::string & refFasta, const std::string & gffFile, double & _pvalues){
std::map<std::string, FastaMeta> metaInformations;
Scorei m(_matchingScore, _mismatchingPenalty);
std::map<std::string, std::string> sequences;
std::vector<std::string> seqNames;
readFastaFile( _input, sequences, metaInformations, seqNames );
Score score(scoreFoler);
std::map<std::string, std::string> sequences0;
std::vector<std::string> seqNames0;
//readFastaFile( "/media/bs674/2t/genomeSequence/maize/Zea_mays.AGPv4.dna.toplevel.fa", sequences0, seqNames0);
readFastaFile( refFasta, sequences0, seqNames0);
std::map<std::string, int32_t> chrSize;
for( std::map<std::string, std::string>::iterator it = sequences0.begin(); it!=sequences0.end(); ++it ){
chrSize[it->first] = it->second.size();
}
std::map<std::string, int16_t *> weight;
std::map<std::string, int16_t *> weight_rev;
//readGffFileWithEveryThing("/media/bs674/2t/genomeSequence/maize/Zea_mays.AGPv3.31.gff3", chrSize, weight, weight_rev);
readGffFileWithEveryThing(gffFile, chrSize, weight, weight_rev);
SequenceCharToUInt8 sequenceCharToUInt8;
std::string refChr = metaInformations[_reference].getChr();
std::string seq1_string = sequences[_reference];
int8_t * seq1 = sequenceCharToUInt8.seq_to_int8(seq1_string);
int8_t * seq1_rev_com = sequenceCharToUInt8.rev_comp(seq1, seq1_string.length());
int32_t length1 = seq1_string.length();
sequences0.clear();
for( std::string _query : seqNames ){
if( _query.compare(_reference) != 0) {
std::string seq2_string = sequences[_query];
int8_t *seq2 = sequenceCharToUInt8.seq_to_int8(seq2_string);
int8_t *seq2_rev_com = sequenceCharToUInt8.rev_comp(seq2, seq2_string.length());
int32_t length2 = seq2_string.length();
std::vector<PairedSimilarFragment> pairedSimilarFragments0 =
findSimilarFragmentsForPairedSequence_wighted_1gap ( seq1, seq1_rev_com,
seq2, seq2_rev_com, length1, length2, _seed_window_size,
_mini_cns_score, _matrix_boundary_distance,
_openGapPenalty1, _extendGapPenalty1, _matchingScore, _mismatchingPenalty,
m, _step_size, seq1_string, seq2_string,
_pvalues, _lambda, _kValue, _zDrop,
_bandwidth, _w, _xDrop, score,
weight[refChr]+metaInformations[_reference].getStart()-1,
weight_rev[refChr] + (chrSize[refChr]-(metaInformations[_reference].getStart()+length1-1)));
if (_onlySyntenic) {
std::vector<PairedSimilarFragment> pairedSimilarFragments = syntenic(pairedSimilarFragments0);
pairedSimilarFragments0 = pairedSimilarFragments;
}
outputNoMasking(_output+metaInformations[_query].getSpecies(), pairedSimilarFragments0, metaInformations[_reference].getStrand(),
metaInformations[_query].getStrand(), metaInformations[_reference].getStart(),
metaInformations[_query].getStart(), metaInformations[_reference].getChr(), metaInformations[_query].getChr(),
seq1_string, seq2_string);
delete seq2;
delete seq2_rev_com;
}
}
delete seq1;
delete seq1_rev_com;
}
int weighted1Gap(int argc, char** argv){
std::stringstream usage;
usage << "Usage: "<<softwareName<<" weighted1Gap -i input -r reference -q query -o output" << std::endl<<
"Options" << std::endl <<
" -i FILE input file in fasta format" << std::endl <<
" -r STRING reference sequence entry name in input fasta file" << std::endl <<
" -f STRING gff3 format reference genome annotation file" << std::endl <<
" -ra STRING masked reference genome sequence in fasta format" << std::endl <<
" -sp STRING the folder where score parameters located" << std::endl <<
// " -q STRING query sequence entry name in input fasta file" << std::endl <<
" -o FILE output file, exists file will be overwrote" << std::endl <<
" -y bool only output syntenic result (default: false)" << std::endl <<
" -A INT Matching score (default: " << matchingScore << ")" << std::endl <<
" -B INT Mismatching penalty (default: " << mismatchingPenalty << ")" << std::endl <<
" -O1 INT open gap penalty (default: " << openGapPenalty1 << ")" << std::endl <<
" -E1 INT extend gap penalty (default: " << extendGapPenalty1 << ")" << std::endl <<
// " -O2 INT open gap penalty (default: " << openGapPenalty2 << ")" << std::endl <<
// " -E2 INT extend gap penalty (default: " << extendGapPenalty2 << ")" << std::endl <<
" -u INT xextend alignment band width (default: " << w << ")" << std::endl <<
//" - INT xextend alignment band width (default: " << extendGapPenalty1 << ")" << std::endl <<
" -w INT the windows size used to run the smith-waterman algorithm to get the alignment seed (default: "<<seed_window_size<<")" << std::endl <<
//" -m INT minimum seeds size to trigger a alignment extension and the minimum conserved sequence to report (default: " << mini_cns_seed_size << ")" << std::endl <<
" -c INT minimum seeds score to trigger a alignment extension (default: " << mini_cns_score << ")" << std::endl <<
" -s INT step size for sliding the smith-waterman seeds alignment window (default: " << step_size << ")" << std::endl <<
" -l DOUBLE lambda value for pvalue caculation (default: " << lambda << ")" << std::endl <<
" -k DOUBLE k value for pvalue caculation (default: " << kValue << ")" << std::endl <<
" -p DOUBLE pvalue for significant alignment output (default: " << pvalues << ")" << std::endl <<
" -b INT minimum number of base-pairs between the maximum smith-waterman score with the score matrix boundary (default: " << matrix_boundary_distance << ") , it is not important" << std::endl;
InputParser inputParser (argc, argv);
if( inputParser.cmdOptionExists("-A") ){
matchingScore = std::stoi( inputParser.getCmdOption("-A") );
}
if( inputParser.cmdOptionExists("-B") ){
mismatchingPenalty = std::stoi( inputParser.getCmdOption("-B") );
}
if( inputParser.cmdOptionExists("-O1") ){
openGapPenalty1 = std::stoi( inputParser.getCmdOption("-O1") );
}
if( inputParser.cmdOptionExists("-E1") ){
extendGapPenalty1 = std::stoi( inputParser.getCmdOption("-E1") );
}
if( inputParser.cmdOptionExists("-u") ){
w = std::stoi( inputParser.getCmdOption("-u") );
}
if( inputParser.cmdOptionExists("-y") ){
onlySyntenic = str2bool( inputParser.getCmdOption("-y"), onlySyntenic );
}
if( inputParser.cmdOptionExists("-w") ){
seed_window_size = std::stoi( inputParser.getCmdOption("-w") );
}
// if( inputParser.cmdOptionExists("-m") ){
// mini_cns_seed_size = std::stoi( inputParser.getCmdOption("-m") );
// }
if( inputParser.cmdOptionExists("-c") ){
mini_cns_score = std::stoi( inputParser.getCmdOption("-c") );
}
if( inputParser.cmdOptionExists("-s") ){
step_size = std::stoi( inputParser.getCmdOption("-s") );
}
if( inputParser.cmdOptionExists("-b") ){
matrix_boundary_distance = std::stoi( inputParser.getCmdOption("-b") );
}
if( inputParser.cmdOptionExists("-l") ){
lambda = std::stod( inputParser.getCmdOption("-l") );
}
if( inputParser.cmdOptionExists("-k") ){
kValue = std::stod( inputParser.getCmdOption("-k") );
}
if( inputParser.cmdOptionExists("-p") ){
pvalues = std::stod( inputParser.getCmdOption("-p") );
}
if(inputParser.cmdOptionExists("-h") ||inputParser.cmdOptionExists("--help") ){
std::cerr << usage.str();
}else if( inputParser.cmdOptionExists("-i") && inputParser.cmdOptionExists("-r") && /*inputParser.cmdOptionExists("-q") &&*/
inputParser.cmdOptionExists("-o") && inputParser.cmdOptionExists("-ra") && inputParser.cmdOptionExists("-sp")
&& inputParser.cmdOptionExists("-f")){
std::string input = inputParser.getCmdOption("-i");
std::string reference = inputParser.getCmdOption("-r");
//std::string query = inputParser.getCmdOption("-q");
std::string output = inputParser.getCmdOption("-o");
std::string refFasta = inputParser.getCmdOption("-ra");
std::string scoreFoler = inputParser.getCmdOption("-sp");
std::string gffFile = inputParser.getCmdOption("-f");
weighted1Gap(input, reference, output, matchingScore, mismatchingPenalty, openGapPenalty1,
extendGapPenalty1,seed_window_size, mini_cns_score,
step_size, matrix_boundary_distance, onlySyntenic, lambda, kValue, bandwidth, w, xDrop, zDrop, scoreFoler,
refFasta, gffFile, pvalues);
return 0;
}else{
std::cerr << usage.str();
}
return 1;
}
void weighted2Gaps(std::string & _input, std::string & _reference, std::string & _output,
int32_t & _matchingScore, int32_t & _mismatchingPenalty, int32_t & _openGapPenalty1,
int32_t & _extendGapPenalty1, int32_t & _seed_window_size, int32_t & _mini_cns_score,
int32_t & _step_size, int32_t & _matrix_boundary_distance, bool & _onlySyntenic, const double & _lambda,
const double & _kValue, int32_t & _w, const int32_t & _bandwidth, const int32_t & _xDrop, const int32_t & _zDrop, const std::string & scoreFoler,
const std::string & refFasta, const std::string & gffFile, double & _pvalues){
std::map<std::string, FastaMeta> metaInformations;
Scorei m(_matchingScore, _mismatchingPenalty);
std::map<std::string, std::string> sequences;
std::vector<std::string> seqNames;
readFastaFile( _input, sequences, metaInformations, seqNames );
Score score(scoreFoler);
std::map<std::string, std::string> sequences0;
std::vector<std::string> seqNames0;
//readFastaFile( "/media/bs674/2t/genomeSequence/maize/Zea_mays.AGPv4.dna.toplevel.fa", sequences0, seqNames0);
readFastaFile( refFasta, sequences0, seqNames0);
std::map<std::string, int32_t> chrSize;
for( std::map<std::string, std::string>::iterator it = sequences0.begin(); it!=sequences0.end(); ++it ){
chrSize[it->first] = it->second.size();
}
std::map<std::string, int16_t *> weight;
std::map<std::string, int16_t *> weight_rev;
//readGffFileWithEveryThing("/media/bs674/2t/genomeSequence/maize/Zea_mays.AGPv3.31.gff3", chrSize, weight, weight_rev);
readGffFileWithEveryThing(gffFile, chrSize, weight, weight_rev);
SequenceCharToUInt8 sequenceCharToUInt8;
std::string refChr = metaInformations[_reference].getChr();
std::string seq1_string = sequences[_reference];
int8_t * seq1 = sequenceCharToUInt8.seq_to_int8(seq1_string);
int8_t * seq1_rev_com = sequenceCharToUInt8.rev_comp(seq1, seq1_string.length());
int32_t length1 = seq1_string.length();
sequences0.clear();
for( std::string _query : seqNames ){
if( _query.compare(_reference) != 0) {
std::string seq2_string = sequences[_query];
int8_t *seq2 = sequenceCharToUInt8.seq_to_int8(seq2_string);
int8_t *seq2_rev_com = sequenceCharToUInt8.rev_comp(seq2, seq2_string.length());
int32_t length2 = seq2_string.length();
std::vector<PairedSimilarFragment> pairedSimilarFragments0 =
findSimilarFragmentsForPairedSequence_wighted ( seq1, seq1_rev_com,
seq2, seq2_rev_com, length1, length2, _seed_window_size,
_mini_cns_score, _matrix_boundary_distance,
_openGapPenalty1, _extendGapPenalty1, _matchingScore, _mismatchingPenalty,
m, _step_size, seq1_string, seq2_string,
_pvalues, _lambda, _kValue, _zDrop,
_bandwidth, _w, _xDrop, score,
weight[refChr]+metaInformations[_reference].getStart()-1,
weight_rev[refChr] + ((chrSize[refChr]-(metaInformations[_reference].getStart()+length1-1))) );
if (_onlySyntenic) {
std::vector<PairedSimilarFragment> pairedSimilarFragments = syntenic(pairedSimilarFragments0);
pairedSimilarFragments0 = pairedSimilarFragments;
}
outputNoMasking(_output+metaInformations[_query].getSpecies(), pairedSimilarFragments0, metaInformations[_reference].getStrand(),
metaInformations[_query].getStrand(), metaInformations[_reference].getStart(),
metaInformations[_query].getStart(), metaInformations[_reference].getChr(), metaInformations[_query].getChr(),
seq1_string, seq2_string);
delete seq2;
delete seq2_rev_com;
}
}
delete seq1;
delete seq1_rev_com;
}
int weighted2Gaps(int argc, char** argv){
std::stringstream usage;
usage << "Usage: "<<softwareName<<" weighted2Gaps -i input -r reference -q query -o output" << std::endl<<
"Options" << std::endl <<
" -i FILE input file in fasta format" << std::endl <<
" -r STRING reference sequence entry name in input fasta file" << std::endl <<
" -f STRING gff3 format reference genome annotation file" << std::endl <<
" -ra STRING masked reference genome sequence in fasta format" << std::endl <<
" -sp STRING the folder where score parameters located" << std::endl <<
// " -q STRING query sequence entry name in input fasta file" << std::endl <<
" -o FILE output file, exists file will be overwrote" << std::endl <<
" -y bool only output syntenic result (default: false)" << std::endl <<
" -A INT Matching score (default: " << matchingScore << ")" << std::endl <<
" -B INT Mismatching penalty (default: " << mismatchingPenalty << ")" << std::endl <<
" -O1 INT open gap penalty (default: " << openGapPenalty1 << ")" << std::endl <<
" -E1 INT extend gap penalty (default: " << extendGapPenalty1 << ")" << std::endl <<
" -u INT xextend alignment band width (default: " << w << ")" << std::endl <<
" -u2 INT z drop alignment band width (default: " << bandwidth << ")" << std::endl <<
//" - INT xextend alignment band width (default: " << extendGapPenalty1 << ")" << std::endl <<
" -w INT the windows size used to run the smith-waterman algorithm to get the alignment seed (default: "<<seed_window_size<<")" << std::endl <<
//" -m INT minimum seeds size to trigger a alignment extension and the minimum conserved sequence to report (default: " << mini_cns_seed_size << ")" << std::endl <<
" -c INT minimum seeds score to trigger a alignment extension (default: " << mini_cns_score << ")" << std::endl <<
" -s INT step size for sliding the smith-waterman seeds alignment window (default: " << step_size << ")" << std::endl <<
" -l DOUBLE lambda value for pvalue caculation (default: " << lambda << ")" << std::endl <<
" -k DOUBLE k value for pvalue caculation (default: " << kValue << ")" << std::endl <<
" -p DOUBLE pvalue for significant alignment output (default: " << pvalues << ")" << std::endl <<
" -b INT minimum number of base-pairs between the maximum smith-waterman score with the score matrix boundary (default: " << matrix_boundary_distance << ") , it is not important" << std::endl;
InputParser inputParser (argc, argv);
if( inputParser.cmdOptionExists("-A") ){
matchingScore = std::stoi( inputParser.getCmdOption("-A") );
}
if( inputParser.cmdOptionExists("-B") ){
mismatchingPenalty = std::stoi( inputParser.getCmdOption("-B") );
}
if( inputParser.cmdOptionExists("-O1") ){
openGapPenalty1 = std::stoi( inputParser.getCmdOption("-O1") );
}
if( inputParser.cmdOptionExists("-E1") ){
extendGapPenalty1 = std::stoi( inputParser.getCmdOption("-E1") );
}
if( inputParser.cmdOptionExists("-u") ){
w = std::stoi( inputParser.getCmdOption("-u") );
}
if( inputParser.cmdOptionExists("-u2") ){
bandwidth = std::stoi( inputParser.getCmdOption("-u2") );
}
if( inputParser.cmdOptionExists("-y") ){
onlySyntenic = str2bool( inputParser.getCmdOption("-y"), onlySyntenic );
}
if( inputParser.cmdOptionExists("-w") ){
seed_window_size = std::stoi( inputParser.getCmdOption("-w") );
}
// if( inputParser.cmdOptionExists("-m") ){
// mini_cns_seed_size = std::stoi( inputParser.getCmdOption("-m") );
// }
if( inputParser.cmdOptionExists("-c") ){
mini_cns_score = std::stoi( inputParser.getCmdOption("-c") );
}
if( inputParser.cmdOptionExists("-s") ){
step_size = std::stoi( inputParser.getCmdOption("-s") );
}
if( inputParser.cmdOptionExists("-b") ){
matrix_boundary_distance = std::stoi( inputParser.getCmdOption("-b") );
}
if( inputParser.cmdOptionExists("-l") ){
lambda = std::stod( inputParser.getCmdOption("-l") );
}
if( inputParser.cmdOptionExists("-k") ){
kValue = std::stod( inputParser.getCmdOption("-k") );
}
if( inputParser.cmdOptionExists("-p") ){
pvalues = std::stod( inputParser.getCmdOption("-p") );
}
if(inputParser.cmdOptionExists("-h") ||inputParser.cmdOptionExists("--help") ){
std::cerr << usage.str();
}else if( inputParser.cmdOptionExists("-i") && inputParser.cmdOptionExists("-r")
&& /*inputParser.cmdOptionExists("-q") &&*/ inputParser.cmdOptionExists("-o")
&& inputParser.cmdOptionExists("-ra") && inputParser.cmdOptionExists("-sp")
&& inputParser.cmdOptionExists("-f")){
std::string input = inputParser.getCmdOption("-i");
std::string reference = inputParser.getCmdOption("-r");
//std::string query = inputParser.getCmdOption("-q");
std::string output = inputParser.getCmdOption("-o");
std::string scoreFoler = inputParser.getCmdOption("-sp");
std::string refFasta = inputParser.getCmdOption("-ra");
std::string gffFile = inputParser.getCmdOption("-f");
weighted2Gaps(input, reference, output, matchingScore, mismatchingPenalty, openGapPenalty1,
extendGapPenalty1, seed_window_size, mini_cns_score,
step_size, matrix_boundary_distance, onlySyntenic, lambda, kValue, w, bandwidth, xDrop, zDrop, scoreFoler,
refFasta, gffFile, pvalues);
return 0;
}else{
std::cerr << usage.str();
}
return 1;
}
void outputMasking(std::string _output, std::vector<PairedSimilarFragment> & pairedSimilarFragments0, int32_t refStrand,
int32_t queStrand, int32_t refStart, int32_t queStart, std::string refChr, std::string queChr,
std::string & seq1_string, std::string & seq2_string, std::string & seq1_0_string, std::string & seq2_0_string){
std::ofstream ofile;
ofile.open(_output+".sam", std::ios_base::app);
std::ofstream ofile2;
ofile2.open(_output+"o", std::ios_base::app);
// ofile << "@SQ\tSN:8\tLN:181122637" << std::endl;
ofile2 << "#" << refChr << ":" << refStrand << ":" << refStart << "-" << queChr << ":" << queStrand << ":" << queStart << std::endl;
for( int32_t i=0; i<pairedSimilarFragments0.size(); ++i ){
if( refStrand==1 && queStrand ==1){
int32_t quePos = queStart + pairedSimilarFragments0[i].getStart2() - 1;
int32_t refPos = refStart + pairedSimilarFragments0[i].getStart1() - 1;
int32_t start = 1;
int32_t end = 1;
int32_t number_of_chr=0;
int32_t number_of_n=0;
int32_t started=0;
for ( int32_t j=0; j<seq2_0_string.size(); ++j ){
if ( seq2_0_string[j] == 'n' ){
++number_of_n;
}else{
++number_of_chr;
}
if ( number_of_chr == pairedSimilarFragments0[i].getStart2() && started==0){
start += j;
quePos += number_of_n;
started=1;
}
if ( number_of_chr == pairedSimilarFragments0[i].getEnd2() ){
end += j;
break;
}
}
number_of_chr=0;
number_of_n=0;
int32_t ref_start = 1;
started=0;
for ( int32_t j=0; j<seq1_0_string.size(); ++j ){
if ( seq1_0_string[j] != 'n' ){
++number_of_chr;
}else{
++number_of_n;
}
if ( number_of_chr == pairedSimilarFragments0[i].getStart1() && started==0){
ref_start += j;
refPos += number_of_n;
break;
}
}
ofile << queChr << "\t0\t" << refChr << "\t" << refPos << "\t" << pairedSimilarFragments0[i].getScore() << "\t" << quePos << "H";
int32_t que_i = start-1; // the index of reference
int32_t ref_i = ref_start-1; // the index of query
std::vector<uint32_t> newCigar;
for( int32_t j=0; j<pairedSimilarFragments0[i].getCigar().size(); ++j ){
uint32_t cigarLength = pairedSimilarFragments0[i].getCigar()[j]>>4;
uint32_t cigarType = pairedSimilarFragments0[i].getCigar()[j]&0xf;
uint32_t op = 0;
uint32_t length = 1;
for ( int32_t h=0; h<cigarLength; ++h ){
op = cigarType;
if( op==0 ){
while( seq1_0_string[ref_i]=='n' ){
op=3;
if( newCigar.empty() || op != (newCigar[newCigar.size() - 1]&0xf) ){
newCigar.push_back(length << 4 | op);
}else{
newCigar[newCigar.size()-1] += length<<4;
}
++ref_i;
}
while( seq2_0_string[que_i]=='n' ){
op=6;
if( newCigar.empty() || op != (newCigar[newCigar.size() - 1]&0xf) ){
newCigar.push_back(length << 4 | op);
}else{
newCigar[newCigar.size()-1] += length<<4;
}
++que_i;
}
++ref_i;
++que_i;
}else if(op==1) {
while( seq2_0_string[que_i]=='n' ){
op=6;
if( newCigar.empty() || op != (newCigar[newCigar.size() - 1]&0xf) ){
newCigar.push_back(length << 4 | op);
}else{
newCigar[newCigar.size()-1] += length<<4;
}
++que_i;
}
++que_i;
}else{
while( seq1_0_string[ref_i]=='n' ){
op=3;
if( newCigar.empty() || op != (newCigar[newCigar.size() - 1]&0xf) ){
newCigar.push_back(length << 4 | op);
}else{
newCigar[newCigar.size()-1] += length<<4;
}
++ref_i;
}
++ref_i;
}
op = cigarType;
if( newCigar.empty() || op != (newCigar[newCigar.size() - 1]&0xf) ){
newCigar.push_back(length << 4 | op);
}else{
newCigar[newCigar.size()-1] += length<<4;
}
}
}
for( int32_t j=0; j<newCigar.size(); ++j ){
uint32_t cigarLength = newCigar[j]>>4;
uint32_t cigarType = newCigar[j]&0xf;
ofile << cigarLength << "MIDDSHI=XB"[cigarType];
}
ofile<< "\t*\t0\t0\t" << getSubSequence(seq2_0_string, start, end) << "\t*" << std::endl;
}else if ( refStrand==1 && queStrand ==0) { // this one should be correct
int32_t quePos = queStart + seq2_0_string.size()-1-pairedSimilarFragments0[i].getEnd2()+1; // this is the position on the positive strand
int32_t refPos = refStart + pairedSimilarFragments0[i].getStart1() - 1;
// int32_t quePos = queStart + pairedSimilarFragments0[i].getStart2() - 1;
// int32_t refPos = refStart + pairedSimilarFragments0[i].getStart1() - 1;
int32_t start = 1;
int32_t end = 1;
int32_t number_of_chr=0;
int32_t number_of_n=0;
int32_t started=0;
for ( int32_t j=0; j<seq2_0_string.size(); ++j ){
if ( seq2_0_string[j] == 'n' ){
++number_of_n;
}else{
++number_of_chr;
}
if ( number_of_chr == pairedSimilarFragments0[i].getStart2() && started==0){
start += j;
started=1;
}
if ( number_of_chr == pairedSimilarFragments0[i].getEnd2() ){
end += j;
quePos -= number_of_n;
break;
}
}
number_of_chr=0;