Fixing potentially dangerous memcpy and cleaning up includes and clang-tidy checks

.clang-tidy

@@ -39,6 +39,7 @@ CheckOptions:
   cppcoreguidelines-rvalue-reference-param-not-moved.AllowPartialMove: 'true'
   cppcoreguidelines-avoid-magic-numbers.IgnoredIntegerValues: '1;2;3;4;10'
   cppcoreguidelines-avoid-magic-numbers.IgnoredFloatingPointValues: '1.0;2.0;10.0;100.0'
+  misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic: true
   google-readability-braces-around-statements.ShortStatementLines: '1'
   google-readability-namespace-comments.ShortNamespaceLines: '10'
   google-readability-namespace-comments.SpacesBeforeComments: '2'

.cppcheck_suppress

@@ -35,7 +35,7 @@ missingInclude
 *:*CLI11.hpp
 *:*json.hpp
 *:*boost_unordered.hpp
-*:fmt/*.h
+*:*fmt/*.h
 # Problem caused by external files
 toomanyconfigs
 # More problems caused by external files -- with too many ifdefs

src/bgzf_reader.cpp

@@ -61,7 +61,7 @@ bgzf_reader::read_data() -> bool {
   if (at_eof())
     return false;
   const auto unused_in = std::distance(next_in, end_in);
-  std::memcpy(inbuf.get(), next_in, unused_in);
+  std::copy_n(next_in, unused_in, inbuf.get());
   next_in = inbuf.get();
   // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
   end_in = next_in + unused_in;

src/contaminant_set.cpp

@@ -11,7 +11,6 @@
 #include <stdexcept>
 #include <string>
 #include <string_view>
-#include <tuple>  // for std::get
 #include <utility>
 #include <vector>
 

src/contaminant_set.hpp

@@ -5,7 +5,6 @@
 
 #include <cstdint>
 #include <iterator>
-#include <ranges>  // for std::pair
 #include <string>
 #include <utility>
 #include <vector>

src/falco.cpp

@@ -345,17 +345,19 @@ main(int argc, char *argv[]) {
     argv = app.ensure_utf8(argv);
     app.usage(
       std::format("Usage: {} [options] -o OUTDIR INFILES", PROJECT_NAME));
+    // NOLINTBEGIN(clang-analyzer-cplusplus.NewDeleteLeaks)
     if (argc >= 2)
       app.footer(std::format(description, falco::get_share_dir()));
+    // NOLINTEND(clang-analyzer-cplusplus.NewDeleteLeaks)
 
     // clang-format off
     // NOLINTNEXTLINE(cppcoreguidelines-avoid-magic-numbers)
     app.get_formatter()->long_option_alignment_ratio(0.2);
     app.set_help_flag("-h,--help", "Print more detailed help");
-    // NOLINTNEXTLINE(clang-analyzer-cplusplus.NewDeleteLeaks)
     app.set_version_flag("--version", VERSION, "Print program version");
-    app.add_flag("--license", [&](auto) {
-      std::print("{}", license_text); throw CLI::Success(); },
+    app.add_flag("--license",
+      // NOLINTNEXTLINE(clang-analyzer-cplusplus.NewDeleteLeaks)
+      [&](auto) { std::print("{}", license_text); throw CLI::Success(); },
       "Print full license")
       ->callback_priority(CLI::CallbackPriority::PreRequirementsCheck);
     auto infiles_opt =

src/falco_analyzer.cpp

@@ -20,7 +20,6 @@
 #include <mutex>
 #include <ranges>
 #include <thread>
-#include <tuple>  // for std::get (iwyu fp)
 #include <utility>
 #include <variant>
 #include <vector>

src/html.cpp

@@ -29,7 +29,6 @@
 #include <span>
 #include <stdexcept>
 #include <string>
-#include <tuple>    // for std::get probably in fmt
 #include <utility>  // for pair
 #include <vector>
 
@@ -371,8 +370,8 @@ basic_stats_html(const file_info &info,
 
 [[nodiscard]] auto
 tile_html(const tile_processor::tiles_centered_t &centered,
-          const std::vector<base_group_t> &groups, const file_grades &grades)
-  -> std::string {
+          const std::vector<base_group_t> &groups,
+          const file_grades &grades) -> std::string {
   static constexpr auto label = "tile";
   static constexpr auto n_quants = 20.0;
   // ADS: ??? (-10: red, 0: light blue, +10: dark blue)

src/report.cpp

@@ -23,6 +23,7 @@
 #include <format>
 #include <iterator>
 #include <limits>
+#include <map>
 #include <numeric>
 #include <ranges>
 #include <span>
@@ -209,8 +210,8 @@ basic_stats_report(const file_info &info,
 
 [[nodiscard]] auto
 tile_report(const tile_processor::tiles_centered_t &centered,
-            const std::vector<base_group_t> &groups, const file_grades &grades)
-  -> std::string {
+            const std::vector<base_group_t> &groups,
+            const file_grades &grades) -> std::string {
   static constexpr auto label = "tile";
   static constexpr auto max_precision{std::numeric_limits<double>::digits10};
   static constexpr auto start_tag = ">>Per tile sequence quality\t{}\n";

src/tile_processor.cpp

@@ -26,7 +26,6 @@
 #include <ranges>
 #include <stdexcept>
 #include <string>
-#include <tuple>  // for std::get
 #include <utility>
 #include <vector>