trying to debug on TACC which means getting ASAN bulit in

CMakeLists.txt

@@ -37,10 +37,10 @@ endif()
 message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
 
 if (${CMAKE_BUILD_TYPE} MATCHES Release)
-    set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG")
-    set(CMAKE_C_FLAGS_RELEASE "-DNDEBUG")
+  #set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG")
+  #  set(CMAKE_C_FLAGS_RELEASE "-DNDEBUG")
     if (NOT EXTRA_FLAGS)
-      set(EXTRA_FLAGS "-Ofast -march=x86-64-v3")
+      set(EXTRA_FLAGS "-Ofast -march=x86-64-v3 -g")
     endif()
 endif ()
 
@@ -103,11 +103,20 @@ ExternalProject_Add(jemalloc
   BUILD_IN_SOURCE 1
 )
 
+ExternalProject_Add(gcc-13.2.0
+  URL https://ftp.gnu.org/gnu/gcc/gcc-13.2.0/gcc-13.2.0.tar.gz
+  PREFIX ${CMAKE_CURRENT_BINARY_DIR}/gcc-13.2.0
+  CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=${CMAKE_CURRENT_BINARY_DIR}/gcc-13.2.0 --enable-languages=c,c++ --disable-multilib --enable-libsanitizer=address
+  BUILD_COMMAND $(MAKE)
+  INSTALL_COMMAND $(MAKE) install
+  BUILD_IN_SOURCE 1
+)
+
 add_executable(wfmash
   src/common/utils.cpp
   src/interface/main.cpp)
 
-add_dependencies(wfmash htslib gsl libdeflate jemalloc)
+add_dependencies(wfmash htslib gsl libdeflate jemalloc gcc-13.2.0)
 
 target_include_directories(wfmash PRIVATE
   src
@@ -135,6 +144,7 @@ target_link_libraries(wfmash
   z
   ${CMAKE_CURRENT_BINARY_DIR}/libdeflate/lib64/libdeflate.a
   Threads::Threads
+  ${CMAKE_CURRENT_BINARY_DIR}/gcc-13.2.0/lib64/libasan.a
 )
 
 configure_file(${CMAKE_SOURCE_DIR}/CTestCustom.cmake ${CMAKE_BINARY_DIR})

src/common/wflign/CMakeLists.txt

@@ -21,8 +21,8 @@ message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
 
 if (${CMAKE_BUILD_TYPE} MATCHES Release)
     #set(EXTRA_FLAGS "-Ofast -march=x86-64-v3 -flto -fno-fat-lto-objects")
-    set(EXTRA_FLAGS "-Ofast -march=x86-64-v3")
-    set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
+    set(EXTRA_FLAGS "-Ofast -march=x86-64-v3 -g")
+    #set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
 endif ()
 
 if (${CMAKE_BUILD_TYPE} MATCHES Debug)

src/common/wflign/src/wflign.cpp

@@ -183,8 +183,8 @@ int wflambda_extend_match(
         if (f != alignments.end()) {
             is_a_match = (alignments[k] != nullptr);
         } else {
-            const int query_begin = v * step_size;
-            const int target_begin = h * step_size;
+            const int64_t query_begin = v * step_size;
+            const int64_t target_begin = h * step_size;
 
             // The last fragment can be longer than segment_length_to_use (max 2*segment_length_to_use - 1)
             const uint16_t segment_length_to_use_q =

src/common/wflign/src/wflign_alignment.cpp

@@ -642,4 +642,4 @@ bool hack_cigar(wfa::cigar_t &cigar, const char *query, const char *target,
         }
     }
     return ok;
-}*/
+}*/

src/common/wflign/src/wflign_patch.cpp

@@ -28,18 +28,25 @@ bool do_wfa_segment_alignment(
         const char* query,
         std::vector<rkmh::hash_t>*& query_sketch,
         const uint64_t& query_length,
-        const int& j,
+        const int64_t& j,
         const std::string& target_name,
         const char* target,
         std::vector<rkmh::hash_t>*& target_sketch,
         const uint64_t& target_length,
-        const int& i,
+        const int64_t& i,
         const uint16_t& segment_length_q,
         const uint16_t& segment_length_t,
         const uint16_t& step_size,
         wflign_extend_data_t* extend_data,
         alignment_t& aln) {
 
+    // if our i or j index plus segment length in the query or target is too long we'll make a memory access error and weird stuff will happen
+    if (i + segment_length_t > target_length || j + segment_length_q > query_length) {
+        // display function parameters
+        std::cerr << "query_name: " << query_name << " query_length: " << query_length << " target_name: " << target_name << " target_length: " << target_length << std::endl;
+        std::cerr << "i: " << i << " j: " << j << " segment_length_t: " << segment_length_t << " segment_length_q: " << segment_length_q << std::endl;
+    }
+
     // first make the sketches if we haven't yet
     if (query_sketch == nullptr) {
         query_sketch = new std::vector<rkmh::hash_t>();
@@ -48,7 +55,7 @@ bool do_wfa_segment_alignment(
         ++extend_data->num_sketches_allocated;
     }
     if (target_sketch == nullptr) {
-        target_sketch = new std::vector<rkmh::hash_t>();
+        target_sketch = new std::vector<rkmh::hash_t>();        
         *target_sketch = rkmh::hash_sequence(
                 target + i, segment_length_t, extend_data->minhash_kmer_size, (uint64_t)((float)segment_length_t * extend_data->mash_sketch_rate));
         ++extend_data->num_sketches_allocated;

src/common/wflign/src/wflign_patch.hpp

@@ -34,12 +34,12 @@ namespace wflign {
                 const char* query,
                 std::vector<rkmh::hash_t>*& query_sketch,
                 const uint64_t& query_length,
-                const int& j,
+                const int64_t& j,
                 const std::string& target_name,
                 const char* target,
                 std::vector<rkmh::hash_t>*& target_sketch,
                 const uint64_t& target_length,
-                const int& i,
+                const int64_t& i,
                 const uint16_t& segment_length_q,
                 const uint16_t& segment_length_t,
                 const uint16_t& step_size,
@@ -120,4 +120,4 @@ namespace wflign {
     void encodeOneStep(const char *filename, std::vector<unsigned char> &image, unsigned width, unsigned height);
 } /* namespace wflign */
 
-#endif /* WFLIGN_PATCH_HPP_ */
+#endif /* WFLIGN_PATCH_HPP_ */