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#include <seqan/store.h>
#include <seqan/realign.h>
using namespace seqan;
int main()
{
// Build paths to reference and to alignment.
std::string refPath = getAbsolutePath("demos/tutorial/realignment/ref.fa");
std::string samPath = getAbsolutePath("demos/tutorial/realignment/reads.sam");
// Declare fragment store.
FragmentStore<> store;
// Load contigs and read alignment.
loadContigs(store, refPath.c_str());
BamFileIn bamFileIn(samPath.c_str());
readRecords(store, bamFileIn);
// Perform the realignment.
reAlignment(store, /*contigID=*/ 0, /*method=*/ 1, /*bandwidth=*/ 20,
/*includeReference=*/ true);
// Layout alignment and print.
AlignedReadLayout layout;
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, /*contigID=*/ 0, /*posBegin=*/ 1060,
/*posEnd=*/ 1140, /*lineBegin=*/ 0, /*lineEnd=*/ 100);
return 0;
}
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