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//![build_index1]
//![open_index1]
#include <seqan/seq_io.h>
#include <seqan/sequence.h>
using namespace seqan2;
int main()
{
CharString pathToFile = getAbsolutePath("/demos/tutorial/indexed_fasta_io/example.fasta");
FaiIndex faiIndex;
//![open_index1]
if (!build(faiIndex, toCString(pathToFile)))
std::cout << "ERROR: Could not build the index!\n";
//![build_index1]
clear(faiIndex);
//![build_index2]
CharString pathToFaiFile = pathToFile;
append(pathToFaiFile, ".fai");
if (!build(faiIndex, toCString(pathToFile), toCString(pathToFaiFile)))
std::cout << "ERROR: Could not build the index!\n";
//![build_index2]
//![save_index]
if (!save(faiIndex, toCString(pathToFaiFile)))
std::cout << "ERROR: Could not save the index to file!\n";
//![save_index]
//![open_index1]
if (!open(faiIndex, toCString(pathToFile)))
std::cout << "ERROR: Could not load FAI index " << pathToFile << ".fai\n";
//![open_index1]
//![open_index2]
if (!open(faiIndex, toCString(pathToFile), toCString(pathToFaiFile)))
std::cout << "ERROR: Could not load FAI index " << pathToFaiFile << "\n";
//![open_index2]
//![idx]
unsigned idx = 0;
if (!getIdByName(idx, faiIndex, "chr1"))
std::cout << "ERROR: FAI index has no entry for chr1.\n";
//![idx]
//![example_functions]
unsigned seqLength = sequenceLength(faiIndex, idx);
// Load first 10 characters of chr1.
CharString seqChr1Prefix;
readRegion(seqChr1Prefix, faiIndex, idx, 0, 10);
// Load all of chr1.
CharString seqChr1;
readSequence(seqChr1, faiIndex, idx);
//![example_functions]
ignoreUnusedVariableWarning(seqLength);
//![example_functions]
return 0;
}
//![example_functions]
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