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// SeqInput.h
#ifndef FLEXBAR_SEQINPUT_H
#define FLEXBAR_SEQINPUT_H
#include <seqan/seq_io.h>
#include "QualTrimming.h"
template <typename TSeqStr, typename TString>
class SeqInput {
private:
seqan::FlexbarReadsSeqFileIn seqFileIn;
const flexbar::QualTrimType m_qtrim;
const flexbar::FileFormat m_format;
const bool m_preProcess, m_useStdin, m_qtrimPostRm, m_iupacInput;
const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize;
std::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred;
public:
SeqInput(const Options &o, const std::string filePath, const bool preProcess, const bool useStdin) :
m_preProcess(preProcess),
m_useStdin(useStdin),
m_maxUncalled(o.maxUncalled),
m_preTrimBegin(o.cutLen_begin),
m_preTrimEnd(o.cutLen_end),
m_qtrim(o.qTrim),
m_qtrimThresh(o.qtrimThresh),
m_qtrimWinSize(o.qtrimWinSize),
m_qtrimPostRm(o.qtrimPostRm),
m_iupacInput(o.iupacInput),
m_format(o.format),
m_nrReads(0),
m_nrChars(0),
m_nLowPhred(0){
using namespace std;
if(m_useStdin){
if(! open(seqFileIn, cin)){
cerr << "\nERROR: Could not open input stream.\n" << endl;
exit(1);
}
}
else{
if(! open(seqFileIn, filePath.c_str())){
cerr << "\nERROR: Could not open file " << filePath << "\n" << endl;
exit(1);
}
}
};
virtual ~SeqInput(){
close(seqFileIn);
};
// returns number of read SeqReads
unsigned int loadSeqReads(seqan::StringSet<bool> &uncalled, flexbar::TStrings &ids, flexbar::TSeqStrs &seqs, flexbar::TStrings &quals, const unsigned int nReads){
using namespace std;
using namespace flexbar;
using seqan::prefix;
using seqan::suffix;
using seqan::length;
try{
if(! atEnd(seqFileIn)){
reserve(ids, nReads);
reserve(seqs, nReads);
reserve(uncalled, nReads);
if(! m_iupacInput){
if(m_format == FASTA){
readRecords(ids, seqs, seqFileIn, nReads);
}
else{
reserve(quals, nReads);
readRecords(ids, seqs, quals, seqFileIn, nReads);
}
}
else{
seqan::StringSet<seqan::IupacString> seqsIupac;
reserve(seqsIupac, nReads);
if(m_format == FASTA){
readRecords(ids, seqsIupac, seqFileIn, nReads);
}
else{
reserve(quals, nReads);
readRecords(ids, seqsIupac, quals, seqFileIn, nReads);
}
seqs = seqsIupac;
}
for(unsigned int i = 0; i < length(ids); ++i){
TString &id = ids[i];
TSeqStr &seq = seqs[i];
if(length(id) < 1){
cerr << "\nERROR: Input read without name.\n" << endl;
close(seqFileIn);
exit(1);
}
if(length(seq) < 1){
cerr << "\nERROR: Input read without sequence.\n" << endl;
close(seqFileIn);
exit(1);
}
m_nrChars += length(seq);
appendValue(uncalled, isUncalledSequence(seq));
if(m_preProcess){
if(m_preTrimBegin > 0 && length(seq) > 1){
int idx = m_preTrimBegin;
if(idx >= length(seq)) idx = length(seq) - 1;
erase(seq, 0, idx);
if(m_format == FASTQ)
erase(quals[i], 0, idx);
}
if(m_preTrimEnd > 0 && length(seq) > 1){
int idx = m_preTrimEnd;
if(idx >= length(seq)) idx = length(seq) - 1;
seq = prefix(seq, length(seq) - idx);
if(m_format == FASTQ)
quals[i] = prefix(quals[i], length(quals[i]) - idx);
}
if(m_qtrim != QOFF && ! m_qtrimPostRm){
if(qualTrim(seq, quals[i], m_qtrim, m_qtrimThresh, m_qtrimWinSize)) ++m_nLowPhred;
}
}
}
m_nrReads += length(ids);
return length(ids);
}
else return 0; // end of file
}
catch(seqan::Exception const &e){
cerr << "\nERROR: " << e.what() << "\nProgram execution aborted.\n" << endl;
close(seqFileIn);
exit(1);
}
}
// returns TRUE if read contains too many uncalled bases
bool isUncalledSequence(TSeqStr &seq){
using namespace seqan;
typename Iterator<TSeqStr>::Type it, itEnd;
it = begin(seq);
itEnd = end(seq);
int n = 0;
while(it != itEnd){
if(*it == 'N') n++;
++it;
}
return(n > m_maxUncalled);
}
unsigned long getNrLowPhredReads() const {
return m_nLowPhred;
}
unsigned long getNrProcessedReads() const {
return m_nrReads;
}
unsigned long getNrProcessedChars() const {
return m_nrChars;
}
};
#endif
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