From dd6c01736f5741d26fa355ce589bb7b51734dde7 Mon Sep 17 00:00:00 2001
From: Milot Mirdita <milot@mirdita.de>
Date: Tue, 31 Oct 2023 13:55:05 +0900
Subject: [PATCH] More CI fixes to be WERROR clean

---
 src/CMakeLists.txt                  | 4 ++--
 src/test/TestAlignmentTraceback.cpp | 8 ++++----
 src/test/TestKsw2.cpp               | 4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 27f6a6979..976ac78a8 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -76,8 +76,8 @@ if (NOT EMSCRIPTEN)
 endif()
 
 if (ENABLE_WERROR)
-    append_target_property(mmseqs-framework COMPILE_FLAGS -Werror)
-    append_target_property(mmseqs-framework LINK_FLAGS -Werror)
+    append_target_property(mmseqs-framework COMPILE_FLAGS -Werror -Wno-unused-command-line-argument)
+    append_target_property(mmseqs-framework LINK_FLAGS -Werror -Wno-unused-command-line-argument)
 endif()
 
 # needed for concat.h
diff --git a/src/test/TestAlignmentTraceback.cpp b/src/test/TestAlignmentTraceback.cpp
index beddd5a7a..6e66bedb7 100644
--- a/src/test/TestAlignmentTraceback.cpp
+++ b/src/test/TestAlignmentTraceback.cpp
@@ -87,16 +87,16 @@ void sw(
     // backtrace
     int i=target_length - 1;
     int j=query_length - 1;
-    int step = 0;
+    // int step = 0;
     int state = get_val(bt, i, j);
-    int matched_cols = 0;
+    // int matched_cols = 0;
     while (state!=-1)     // while (state!=STOP)  because STOP=0
     {
-        step++;
+        // step++;
         //std::cout << step<< " " << i << " " << j << " " << state << std::endl;
         switch (state) {
             case M: // current state is MM, previous state is bMM[i][j]
-                matched_cols++;
+                // matched_cols++;
                 fprintf(stdout,"%c", subMat.num2aa[db_sequence[target_start+i]]);
                 if(query_sequence[query_start + j] == db_sequence[target_start + i]){
                     fprintf(stdout, "|");
diff --git a/src/test/TestKsw2.cpp b/src/test/TestKsw2.cpp
index 8f3678023..21f130df0 100644
--- a/src/test/TestKsw2.cpp
+++ b/src/test/TestKsw2.cpp
@@ -255,7 +255,7 @@ void align(const char * qSeqAscii, uint8_t *qseq, uint8_t *qseqrev, const int qL
     std::string middleAln;
     int queryPos = qStartPos;
     int targetPos = tStartPos;
-    int aaIds = 0;
+    // int aaIds = 0;
     for(int i = 0; i < ezAlign.n_cigar; i++){
         int len = ezAlign.cigar[i]>>4;
         switch("MID"[ezAlign.cigar[i]&0xf]){
@@ -264,7 +264,7 @@ void align(const char * qSeqAscii, uint8_t *qseq, uint8_t *qseqrev, const int qL
                 queryAln.push_back(qSeqAscii[queryPos]);
                 if (qSeqAscii[queryPos] == tSeqAscii[targetPos]) {
                     middleAln.push_back('|');
-                    aaIds++;
+                    // aaIds++;
                 } else {
                     middleAln.push_back('*');
                 }