From 6267ffba554845c1b284de3f665d2b143fa81a55 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Tue, 14 May 2024 18:22:10 +0800 Subject: [PATCH] Fix realignment coverage --- src/alignment/Alignment.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/alignment/Alignment.cpp b/src/alignment/Alignment.cpp index 384dcc2b9..59625c842 100644 --- a/src/alignment/Alignment.cpp +++ b/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) {