Fix realignment coverage

Author: milot-mirdita

src/alignment/Alignment.cpp

@@ -419,7 +419,7 @@ void Alignment::run(const std::string &outDB, const std::string &outDBIndex, con
 
                         // recompute alignment boundaries (without changing evalue)
                         const bool isIdentity = (queryDbKey == swResults[result].dbKey && (includeIdentity || sameQTDB)) ? true : false;
-                        Matcher::result_t res = realigner->getSWResult(&dbSeq, INT_MAX, false, realignCov, covThr, FLT_MAX, realignSwMode, seqIdMode, isIdentity);
+                        Matcher::result_t res = realigner->getSWResult(&dbSeq, INT_MAX, false, covMode, realignCov, FLT_MAX, realignSwMode, seqIdMode, isIdentity);
 
                         const bool covOK = Util::hasCoverage(realignCov, covMode, res.qcov, res.dbcov);
                         if (covOK == true || isIdentity) {