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#ifndef APPS_BS_TOOLS_FOUR2THREE_H_
#define APPS_BS_TOOLS_FOUR2THREE_H_
#include <iostream>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>
#include <fstream>
using namespace std;
using namespace seqan2;
struct ConvertCT : public ::std::function<char(char)>
{
inline char operator()(char x) const
{
if (('C' == x) || (x == 'c')) return ('T');
return x;
}
};
struct ConvertGA : public ::std::function<char(char)>
{
inline char operator()(char x) const
{
if (('G' == x) || (x == 'g')) return ('A');
return x;
}
};
template<typename TOptions>
bool
preProcess(TOptions &options)
{
typedef ModifiedString< CharString, ModView<ConvertCT> > TModCT;
typedef ModifiedString< CharString, ModView<ConvertGA> > TModGA;
CharString id, seq, quals;
seqan2::SeqFileIn seqFileIn(toCString(options.inputFileName));
seqan2::SeqFileOut seqFileOut(toCString(options.outputFileName));
// Get lower case of the output file name. File endings are accepted in both upper and lower case.
CharString tmp = options.inputFileName;
toLower(tmp);
if (endsWith(tmp, ".fa") || endsWith(tmp, ".fasta")) // FASTA
{
while (!atEnd(seqFileIn))
{
readRecord(id, seq, seqFileIn);
if (options.ctConversion) // CT
{
TModCT modCT(seq);
CharString tmp = modCT;
writeRecord(seqFileOut, id, tmp);
}
else // GA
{
TModGA modGA(seq);
CharString tmp = modGA;
writeRecord(seqFileOut, id, tmp);
}
}
}
else if (endsWith(tmp, ".fastq") || endsWith(tmp, ".fq")) // FASTQ
{
while (!atEnd(seqFileIn))
{
readRecord(id, seq, quals, seqFileIn);
if (options.ctConversion) //CT
{
TModCT modCT(seq);
CharString tmp = modCT;
writeRecord(seqFileOut, id, tmp, quals);
}
else // GA
{
TModGA modGA(seq);
CharString tmp = modGA;
writeRecord(seqFileOut, id, tmp, quals);
}
}
}
else
{
std::cerr << "ERROR: Something wrong with input!\n";
return 1;
}
return 0;
}
#endif
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