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#include <iostream>
#include <seqan/store.h>
#include <seqan/misc/interval_tree.h>
#include <seqan/parallel.h>
using namespace seqan;
// define used types
typedef FragmentStore<> TStore;
//
// 2. Load annotations and alignments from files
//
bool loadFiles(TStore & store, std::string const & annotationFileName, std::string const & alignmentFileName)
{
// INSERT YOUR CODE HERE ...
//
return true;
}
//![main]
int main(int argc, char const * argv[])
{
TStore store;
std::string annotationFileName = getAbsolutePath("demos/tutorial/simple_rna_seq/example.gtf");
std::string alignmentFileName = getAbsolutePath("demos/tutorial/simple_rna_seq/example.sam");
if (!loadFiles(store, annotationFileName, annotationFileName))
return 1;
return 0;
}
//![main]
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