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#include <seqan/bam_io.h>
using namespace seqan2;
int main(int, char const **)
{
CharString bamFileInName = getAbsolutePath("demos/tutorial/file_io_overview/example.bam");
CharString samFileOutName = getAbsolutePath("demos/tutorial/file_io_overview/example.sam");
// Open input BAM file.
BamFileIn bamFileIn;
if (!open(bamFileIn, toCString(bamFileInName)))
{
std::cerr << "ERROR: could not open input file " << bamFileInName << ".\n";
return 1;
}
// Open output SAM file.
BamFileOut samFileOut(context(bamFileIn), toCString(samFileOutName));
// Copy header.
BamHeader header;
try
{
readHeader(header, bamFileIn);
writeHeader(samFileOut, header);
}
catch (ParseError const & e)
{
std::cerr << "ERROR: input header is badly formatted. " << e.what() << "\n";
}
catch (IOError const & e)
{
std::cerr << "ERROR: could not copy header. " << e.what() << "\n";
}
// Copy all records.
BamAlignmentRecord record;
while (!atEnd(bamFileIn))
{
try
{
readRecord(record, bamFileIn);
writeRecord(samFileOut, record);
}
catch (ParseError const & e)
{
std::cerr << "ERROR: input record is badly formatted. " << e.what() << "\n";
}
catch (IOError const & e)
{
std::cerr << "ERROR: could not copy record. " << e.what() << "\n";
}
}
return 0;
}
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