From 8b5c0e9c06cf537b7123aa09b851d59fd8b41b30 Mon Sep 17 00:00:00 2001
From: Juraj Ahel <juraj.ahel@gmail.com>
Date: Wed, 19 Apr 2023 04:46:17 +0200
Subject: [PATCH] make it so that pairaln requires only .idx_mapping if .idx
 input is used, instead of requiring both .idx_mapping and _mapping

---
 src/util/pairaln.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/util/pairaln.cpp b/src/util/pairaln.cpp
index d400f9dba..5b587a67d 100644
--- a/src/util/pairaln.cpp
+++ b/src/util/pairaln.cpp
@@ -38,8 +38,8 @@ int pairaln(int argc, const char **argv, const Command& command) {
         fileToIds[lookup[i].fileNumber].push_back(lookup[i].id);
     }
 
-    std::string db2NoIndexName = PrefilteringIndexReader::dbPathWithoutIndex(par.db2);
-    MappingReader* mapping = new MappingReader(db2NoIndexName);
+    std::string db2Name = par.db2;
+    MappingReader* mapping = new MappingReader(db2Name);
 
     DBReader<unsigned int> alnDbr(par.db3.c_str(), par.db3Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA);
     alnDbr.open(DBReader<unsigned int>::NOSORT);