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#include <seqan/basic.h>
#include <seqan/index.h>
#include <seqan/sequence.h>
// Test SWIFT finder with empty pattern.
SEQAN_DEFINE_TEST(test_index_swift_find_empty_pattern)
{
using namespace seqan;
typedef Finder<Dna5String, Swift<SwiftSemiGlobal> > TSwiftFinder;
typedef Dna5String TReadSeq_;
typedef StringSet<TReadSeq_> TReadSet;
typedef typename Value<TReadSet>::Type TReadSeq;
typedef typename Value<TReadSeq>::Type TAlphabet;
typedef Shape<TAlphabet, UngappedShape<10> > TShape;
typedef Index<TReadSet, IndexQGram<TShape, OpenAddressing> > TQGramIndex;
typedef Pattern<TQGramIndex, Swift<SwiftSemiGlobal> > TSwiftPattern;
Dna5String contigSeq = "CGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT";
StringSet<Dna5String> readSeqs;
TQGramIndex index(readSeqs);
TSwiftPattern swiftPattern(index);
TSwiftFinder swiftFinder(contigSeq);
while (find(swiftFinder, swiftPattern, 0.1))
continue;
}
SEQAN_BEGIN_TESTSUITE(test_index_swift)
{
SEQAN_CALL_TEST(test_index_swift_find_empty_pattern);
}
SEQAN_END_TESTSUITE
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