Fix missing includes, exception handing nitpicks, and add Nix support

README.md

@@ -112,6 +112,43 @@ If you would like to use an unreleased version of vcf-validator, you can clone t
 
 If you plan to make changes, make sure to check the [docs/developer-guide.md](docs/developer-guide.md).
 
+### Nix
+
+[Nix](https://nixos.org/) is a package manager that provides reproducible environments across Linux, macOS, and Windows (via WSL2).
+
+#### Running without installation
+
+You can run vcf-validator directly from GitHub without cloning or installing dependencies:
+
+```bash
+# Run the validator
+nix run github:EBIvariation/vcf-validator -- --help
+
+# Run the assembly checker  
+nix run github:EBIvariation/vcf-validator#vcf_assembly_checker -- --help
+```
+
+#### Development
+
+For local development with all dependencies pre-installed:
+
+```bash
+# Clone and enter development shell
+git clone https://github.com/EBIvariation/vcf-validator.git
+cd vcf-validator
+nix develop
+
+# Build locally
+mkdir build && cd build
+cmake -DSTATIC_BUILD=OFF ..
+make
+
+# Or build with Nix
+nix build
+```
+
+The development shell includes CMake, Boost, and C++ linters (clang-tidy, cppcheck) ready to use.
+
 ### Linux
 
 The build has been tested on the following compilers:

flake.nix

@@ -0,0 +1,101 @@
+{
+  description = "VCF Validator - Validation suite for Variant Call Format (VCF) files";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    flake-utils.url = "github:numtide/flake-utils";
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = nixpkgs.legacyPackages.${system};
+      in
+      {
+        packages.default = pkgs.stdenv.mkDerivation rec {
+          pname = "vcf-validator";
+          version = "0.10.2";
+
+          src = ./.;
+
+          nativeBuildInputs = with pkgs; [
+            cmake
+            pkg-config
+          ];
+
+          buildInputs = with pkgs; [
+            boost
+            curl
+            openssl
+            zlib
+            bzip2
+          ];
+
+          cmakeFlags = [
+            "-DSTATIC_BUILD=OFF"
+            "-DCMAKE_BUILD_TYPE=Release"
+          ];
+
+          enableParallelBuilding = true;
+
+          installPhase = ''
+            runHook preInstall
+
+            mkdir -p $out/bin
+            cp bin/vcf_validator $out/bin/
+            cp bin/vcf_assembly_checker $out/bin/
+
+            runHook postInstall
+          '';
+
+          doCheck = true;
+          checkPhase = ''
+            runHook preCheck
+            ctest --output-on-failure
+            runHook postCheck
+          '';
+
+          meta = with pkgs.lib; {
+            description = "Validation suite for Variant Call Format (VCF) files";
+            homepage = "https://github.com/EBIvariation/vcf-validator";
+            license = licenses.asl20;
+            maintainers = [ ];
+            platforms = platforms.unix;
+          };
+        };
+
+        apps.default = {
+          type = "app";
+          program = "${self.packages.${system}.default}/bin/vcf_validator";
+        };
+
+        apps.vcf_validator = {
+          type = "app";
+          program = "${self.packages.${system}.default}/bin/vcf_validator";
+        };
+
+        apps.vcf_assembly_checker = {
+          type = "app";
+          program = "${self.packages.${system}.default}/bin/vcf_assembly_checker";
+        };
+
+        devShells.default = pkgs.mkShell {
+          inputsFrom = [ self.packages.${system}.default ];
+          packages = with pkgs; [
+            # Debugging tools
+            gdb
+            valgrind
+
+            # Linters and static analysis
+            clang-tools    # clang-tidy, clang-format
+            cppcheck       # C++ static analyzer
+            include-what-you-use  # Include optimization
+            cpplint        # Google's C++ style checker
+
+            # Build tools
+            bear           # Generates compile_commands.json for clang tools
+            ninja          # Faster builds
+          ];
+        };
+      });
+}

src/fasta/faidx.cpp

@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+#include <cstdint>
 #include <fstream>
 #include <memory>
 #include <string>

src/vcf/assembly_checker.cpp

@@ -139,7 +139,7 @@ namespace ebi
                   try {
                       fasta->sequence(contig, 0, 1);
                   }
-                  catch(ebi::util::curl::URLRetrievalException ex) {
+                  catch(const ebi::util::curl::URLRetrievalException& ex) {
                       std::string warningMessage = "Could not download sequence for contig/chromosome "
                                                    + contig + " because: " + ex.what();
                       write_warning_output(outputs, warningMessage);
@@ -250,7 +250,7 @@ namespace ebi
                   try {
                       fasta->sequence(contig_name, 0, 1); // trigger download
                   }
-                  catch(ebi::util::curl::URLRetrievalException ex) {
+                  catch(const ebi::util::curl::URLRetrievalException& ex) {
                       report_missing_chromosome_in_ENA(line_num, ex.what(), record_core, outputs);
                       is_valid = false;
                       continue;

src/vcf/record.cpp

@@ -261,7 +261,7 @@ namespace ebi
                     try {
                         check_info_field_cardinality(values, key_values[NUMBER]);
                         check_field_type(values, key_values[TYPE]);
-                    } catch (std::shared_ptr<Error> ex) {
+                    } catch (const std::shared_ptr<Error>& ex) {
                         std::string message = "INFO " + key_values[ID] + " does not match the meta" + ex->message;
                         throw new InfoBodyError{line, message, key_values[ID] + "=" + field.second,
                                 ErrorFix::IRRECOVERABLE_VALUE, key_values[ID]};
@@ -280,7 +280,7 @@ namespace ebi
                     } else {
                         check_predefined_tag_info(field.first, values, info_v44);
                     }
-                } catch (std::shared_ptr<Error> ex) {
+                } catch (const std::shared_ptr<Error>& ex) {
                     throw new InfoBodyError{line, "INFO " + ex->message, field.first + "=" + field.second, ErrorFix::IRRECOVERABLE_VALUE, field.first};
                 }
             }
@@ -383,7 +383,7 @@ namespace ebi
             try {
                 check_info_field_cardinality(values, get_predefined_number(iterator));
                 check_field_type(values, get_predefined_type(iterator));
-            } catch (std::shared_ptr<Error> ex) {
+            } catch (const std::shared_ptr<Error>& ex) {
                 raise(std::make_shared<Error>(line, field_key + " does not match the" + ex->message));
             }
             if (get_predefined_type(iterator) == INTEGER) {
@@ -402,7 +402,7 @@ namespace ebi
                 long cardinality;
                 check_sample_field_cardinality(values, get_predefined_number(iterator), ploidy, cardinality);
                 check_field_type(values, get_predefined_type(iterator));
-            } catch (std::shared_ptr<Error> ex) {
+            } catch (const std::shared_ptr<Error>& ex) {
                 raise(std::make_shared<Error>(line, field_key + " does not match the" + ex->message,
                                               ex->detailed_message));
             }
@@ -838,7 +838,7 @@ namespace ebi
                 try {
                     check_sample_field_cardinality(values, meta_entry_properties[NUMBER], ploidy, expected_cardinality);
                     check_field_type(values, meta_entry_properties[TYPE]);
-                } catch (std::shared_ptr<Error> ex) {
+                } catch (const std::shared_ptr<Error>& ex) {
                     std::string message = "Sample #" + std::to_string(i + 1) + ", field " + meta_entry_properties[ID]
                                           + " does not match the meta" + ex->message;
                     std::string detailed_message = meta_entry_properties[ID] + "=" + subfield + ex->detailed_message;
@@ -854,7 +854,7 @@ namespace ebi
                     } else {
                         check_predefined_tag_format(format[j], values, format_v44, ploidy);
                     }
-                } catch (std::shared_ptr<Error> ex) {
+                } catch (const std::shared_ptr<Error>& ex) {
                     throw new SamplesFieldBodyError{line, "Sample #" + std::to_string(i + 1) + ", " + ex->message,
                                                     format[j] + "=" + subfield, format[j]};
                 }
@@ -1070,7 +1070,7 @@ namespace ebi
             // ...try to cast to float
             try {
                 std::stof(value);
-            } catch (std::out_of_range) {
+            } catch (const std::out_of_range&) {
                 // It maybe a subnormal number
                 std::stold(value);
             }

src/vcf/store_parse_policy.cpp

@@ -212,7 +212,7 @@ namespace ebi
         try {
             // Transform the position token into a size_t
             position = static_cast<size_t>(std::stoi(m_line_tokens[POS][0]));
-        } catch (std::invalid_argument ex) {
+        } catch (const std::invalid_argument&) {
             throw new PositionBodyError{state.n_lines};
         }
 
@@ -221,7 +221,7 @@ namespace ebi
         if (m_line_tokens[QUAL][0] != MISSING_VALUE) {
             try {
                 quality = std::stof(m_line_tokens[QUAL][0]);
-            } catch (std::invalid_argument ex) {
+            } catch (const std::invalid_argument&) {
                 throw new QualityBodyError{state.n_lines};
             }
         }
@@ -271,7 +271,7 @@ namespace ebi
     {
         try {
             return m_line_tokens.at(column);
-        } catch (std::out_of_range) {
+        } catch (const std::out_of_range&) {
             return {};
         }
     }