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//![includes]
#define SEQAN_PROFILE // enable time measurements
#include <seqan/seq_io.h>
#include <iostream>
using namespace seqan;
//![includes]
//![open_file]
int main(int argc, char const * argv[])
{
SEQAN_PROTIMESTART(loadTime);
SeqFileIn seqFile;
if (argc < 2 || !open(seqFile, argv[1]))
return 1;
//![open_file]
//![read_sequences]
StringSet<String<Dna5Q> > seqs;
StringSet<CharString> seqIDs;
String<Dna5Q> seq;
CharString qual;
CharString id;
size_t seqCount = 0;
for (; !atEnd(seqFile); ++seqCount)
{
readRecord(id, seq, qual, seqFile); // read record
// convert ascii to values from 0..62
// store dna and quality together in Dna5Q
assignQualities(seq, qual);
// we use reserve and append, as assign is not supported
// by StringSet<..., Owner<ConcatDirect<> > >
appendValue(seqs, seq, Generous());
appendValue(seqIDs, id, Generous());
}
//![read_sequences]
//![output]
std::cout << "Loading " << seqCount << " sequences took " << SEQAN_PROTIMEDIFF(loadTime);
std::cout << " seconds." << std::endl << std::endl;
for (unsigned i = 0; i < seqCount && i < 10; ++i)
{
std::cout << '>' << seqIDs[i] << std::endl;
std::cout << seqs[i] << std::endl;
}
return 0;
}
//![output]
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