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#include <seqan/basic.h>
#include <seqan/seq_io.h>
#include <seqan/sequence.h>
using namespace seqan2;
int main()
{
CharString path = getAbsolutePath("demos/dox/seq_io/example.fa");
FaiIndex faiIndex;
// Try to read the FAI index.
if (!open(faiIndex, toCString(path)))
{
std::cerr << "Could not read the FAI index. Not fatal, we can just build it.\n";
return 1;
}
// Try to build the FAI index (in memory) if reading was unsuccessful. If
// building into memory succeeded, we try to write it out.
if (!build(faiIndex, toCString(path)))
{
std::cerr << "FATAL: Could not build FAI index.\n";
return 1;
}
if (!save(faiIndex))
{
std::cerr << "FATAL: Could not write out FAI index after building.\n";
return 1;
}
// Now, read the first 1000 characters of chr1.
unsigned idx = 0;
if (!getIdByName(idx, faiIndex, "chr"))
{
std::cerr << "FATAL: chr1 not found in FAI index.\n";
return 1;
}
CharString seq;
readRegion(seq, faiIndex, idx, 0, 100);
// Now print the first 100 characters we just read.
std::cout << "chr:1-100 = " << seq << "\n";
return 0;
}
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