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#include <iostream>
#include <seqan/basic.h>
#ifndef STDLIB_VS
#include <seqan/blast.h>
using namespace seqan2;
int main(int argc, char **argv)
{
if (argc != 2)
{
std::cerr << "USAGE: FILE_IN\n";
return 0;
}
typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps;
typedef BlastMatch<TGaps, TGaps> TBlastMatch;
typedef BlastRecord<TBlastMatch> TBlastRecord;
typedef BlastIOContext<> TContext;
BlastTabularFileIn<TContext> file(argv[1]);
readHeader(file);
TBlastRecord record;
while (onRecord(file))
{
// read the record
readRecord(record, file);
// print some diagnostics
std::cout << "Record of query sequence \"" << record.qId << "\"\n"
<< "==========================================\n"
<< "Number of HSPs: " << length(record.matches) << "\n";
if (!empty(record.matches))
std::cout << "BitScore of best HSP: " << front(record.matches).bitScore << "\n";
// print column composition
std::cout << "Columns: ";
for (auto field : context(file).fields)
std::cout << BlastMatchField<>::optionLabels[(int)field] << " ";
std::cout << "\n\n";
// if there is anything unexpected, tell the user about it
if (!empty(context(file).conformancyErrors))
{
std::cout << "There were non critical errors when reading the record:\n";
write(std::cout, context(file).conformancyErrors);
std::cout << "\n\n";
}
if (!empty(context(file).otherLines))
{
std::cout << "There were unidentified lines in the comments:\n";
write(std::cout, context(file).otherLines);
std::cout << "\n\n";
}
std::cout << "\n\n";
}
readFooter(file);
std::cout << "File Format: tabular"
<< (context(file).tabularSpec == BlastTabularSpec::COMMENTS ? " with coment lines" : "")
<< '\n'
<< "Generation: "
<< (context(file).legacyFormat ? " legacy" : " BLAST+")
<< '\n'
<< "Program and version: "
<< context(file).versionString
<< '\n'
<< "Database: "
<< context(file).dbName
<< "\n\n";
return 0;
}
#else
int main()
{
std::cerr << "USAGE: FILE_IN\n";
return 0;
}
#endif
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