Add a debugging compilation option for showing list of NAMs

CMakeLists.txt

@@ -5,6 +5,7 @@ include(FetchContent)
 
 option(ENABLE_AVX "Enable AVX2 support" OFF)
 option(PYTHON_BINDINGS "Build Python bindings" OFF)
+option(TRACE "Highly verbose debugging output" OFF)
 
 find_package(ZLIB)
 find_package(Threads)
@@ -69,6 +70,10 @@ target_link_libraries(salib PUBLIC ZLIB::ZLIB Threads::Threads zstr::zstr)
 IF(ENABLE_AVX)
   target_compile_options(salib PUBLIC "-mavx2")
 ENDIF()
+if (TRACE)
+   target_compile_definitions(salib PUBLIC "TRACE")
+endif()
+
 add_dependencies(salib version)
 
 add_executable(strobealign src/main.cpp)

CONTRIBUTING.md

@@ -17,7 +17,18 @@ more focused discussion.
 When compiling strobealign, you can add `-DCMAKE_BUILD_TYPE=RelWithDebInfo` to
 the `cmake` options to get debug symbols.
 
-If needed, run `make` with `VERBOSE=1` to get more logging output.
+If needed, run `make` with `VERBOSE=1` to get more logging output at build
+time.
+
+To get more logging output when running strobealign, add the `-v` option to
+the command line.
+
+Add `--details` to get more detailed SAM output with some
+strobealign-specific tags added to each alignment record.
+(See below.)
+
+To get even more verbose output, add `-DTRACE=ON` to your CMake options and
+re-compile strobealign. This outputs a list of the found NAMs for each read.
 
 ## Testing
 

src/aln.cpp

@@ -1059,6 +1059,18 @@ void align_or_map_paired(
         nams_pair[is_revcomp] = nams;
     }
 
+#ifdef TRACE
+    for (int is_revcomp : {0, 1}) {
+        const auto& record = is_revcomp == 0 ? record1 : record2;
+        std::cerr << "R" << is_revcomp + 1 << " name: " << record.name << '\n';
+        const auto& nams = nams_pair[is_revcomp];
+        std::cerr << "Found " << nams.size() << " NAMs\n";
+        for (auto& nam : nams) {
+            std::cerr << "- " << nam << '\n';
+        }
+    }
+#endif
+
     Timer extend_timer;
     if (map_param.output_format != OutputFormat::SAM) { // PAF or abundance
         Nam nam_read1;
@@ -1185,6 +1197,13 @@ void align_or_map_single(
     shuffle_top_nams(nams, random_engine);
     statistics.tot_sort_nams += nam_sort_timer.duration();
 
+#ifdef TRACE
+    std::cerr << "Query: " << record.name << '\n';
+    std::cerr << "Found " << nams.size() << " NAMs\n";
+    for (auto& nam : nams) {
+        std::cerr << "- " << nam << '\n';
+    }
+#endif
 
     Timer extend_timer;
     size_t n_best = 0;

src/cmdline.hpp

@@ -7,7 +7,13 @@
 
 struct CommandLineOptions {
     int n_threads { 1 };
-    int chunk_size { 10000 };
+    int chunk_size {
+#ifdef TRACE
+        1
+#else
+        10000
+#endif
+    };
 
     // Input/output
     std::string output_file_name;