feat: compiling on windows

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "duckdb"]
+	path = duckdb
+	url = https://github.com/duckdb/duckdb.git

CMakeLists.txt

@@ -0,0 +1,79 @@
+cmake_minimum_required(VERSION 3.2)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# Set extension name here
+set(TARGET_NAME exon)
+set(EXTENSION_NAME ${TARGET_NAME}_extension)
+set(CMAKE_CXX_STANDARD 11)
+
+project(${TARGET_NAME})
+
+
+Include(FetchContent)
+
+FetchContent_Declare(
+  arrow
+  GIT_REPOSITORY https://github.com/apache/arrow.git
+  GIT_TAG apache-arrow-11.0.0
+)
+
+FetchContent_Declare(
+  httplib
+  GIT_REPOSITORY https://github.com/yhirose/cpp-httplib.git
+  GIT_TAG v0.12.0
+)
+
+FetchContent_Declare(
+  json
+  URL https://github.com/nlohmann/json/releases/download/v3.11.2/json.tar.xz
+)
+
+FetchContent_Declare(
+  Corrosion
+  GIT_REPOSITORY https://github.com/corrosion-rs/corrosion.git
+  GIT_TAG v0.3.5
+)
+
+FetchContent_Declare(
+  spdlog
+  GIT_REPOSITORY https://github.com/gabime/spdlog.git
+  GIT_TAG v1.11.0
+)
+
+list(APPEND available_contents httplib json Corrosion spdlog arrow)
+
+FetchContent_MakeAvailable(${available_contents})
+
+corrosion_import_crate(MANIFEST_PATH rust/Cargo.toml
+  PROFILE release
+)
+
+include_directories(exon/include)
+add_subdirectory(exon/src)
+
+add_library(${EXTENSION_NAME} STATIC ${EXTENSION_SOURCES})
+
+# Build extensions
+set(PARAMETERS "-warnings")
+build_loadable_extension(${TARGET_NAME} ${PARAMETERS} ${EXTENSION_SOURCES})
+
+find_package(OpenSSL REQUIRED)
+message("-- wtt: Found openssl ${OPENSSL_VERSION}")
+
+target_link_libraries(${EXTENSION_NAME}
+  PUBLIC
+  "${CMAKE_CURRENT_BINARY_DIR}/Release/rust.lib"
+  ntdll
+  Secur32
+  OpenSSL::SSL
+  OpenSSL::Crypto
+  bcrypt
+  ncrypt
+  Userenv)
+
+
+install(
+  TARGETS ${EXTENSION_NAME}
+  EXPORT "${DUCKDB_EXPORT_SET}"
+  LIBRARY DESTINATION "${INSTALL_LIB_DIR}"
+  ARCHIVE DESTINATION "${INSTALL_LIB_DIR}")

Makefile

@@ -1,3 +1,35 @@
 pull:
 	git submodule init
 	git submodule update --recursive --remote
+
+
+MKFILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST)))
+PROJ_DIR := $(dir $(MKFILE_PATH))
+
+OSX_BUILD_UNIVERSAL_FLAG=
+ifeq (${OSX_BUILD_UNIVERSAL}, 1)
+	OSX_BUILD_UNIVERSAL_FLAG=-DOSX_BUILD_UNIVERSAL=1
+endif
+ifeq (${STATIC_LIBCPP}, 1)
+	STATIC_LIBCPP=-DSTATIC_LIBCPP=TRUE
+endif
+
+ifeq ($(GEN),ninja)
+	GENERATOR=-G "Ninja"
+	FORCE_COLOR=-DFORCE_COLORED_OUTPUT=1
+endif
+
+BUILD_FLAGS=-DEXTENSION_STATIC_BUILD=1 ${OSX_BUILD_UNIVERSAL_FLAG} ${STATIC_LIBCPP}
+ifeq (${BUILD_SHELL}, 0)
+	BUILD_FLAGS += -DBUILD_SHELL=0
+endif
+
+CLIENT_FLAGS :=
+
+# These flags will make DuckDB build the extension
+EXTENSION_FLAGS=-DENABLE_SANITIZER=OFF -DDUCKDB_OOT_EXTENSION_NAMES="exon" -DDUCKDB_OOT_EXTENSION_EXON_PATH="$(PROJ_DIR)" -DDUCKDB_OOT_EXTENSION_EXON_SHOULD_LINK="TRUE" -DDUCKDB_OOT_EXTENSION_EXON_INCLUDE_PATH="$(PROJ_DIR)exon/include"
+
+release:
+	mkdir -p build/release && \
+	cmake $(GENERATOR) $(FORCE_COLOR) $(EXTENSION_FLAGS) ${CLIENT_FLAGS} -DEXTENSION_STATIC_BUILD=1 -DCMAKE_BUILD_TYPE=Release ${BUILD_FLAGS} -S ./duckdb/ -B build/release && \
+	cmake --build build/release --config Release

exon/include/exon/sam_functions/module.hpp

@@ -0,0 +1,34 @@
+// Copyright 2023 WHERE TRUE Technologies.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#pragma once
+
+#include <duckdb.hpp>
+#include <duckdb/parser/parsed_data/create_scalar_function_info.hpp>
+#include <duckdb/parser/parsed_data/create_table_function_info.hpp>
+#include <duckdb/parser/parsed_data/create_copy_function_info.hpp>
+#include <duckdb/parser/tableref/table_function_ref.hpp>
+
+namespace exon
+{
+
+    class SamFunctions
+    {
+    public:
+        static duckdb::unique_ptr<duckdb::CreateScalarFunctionInfo> GetParseCIGARStringFunction();
+        static duckdb::unique_ptr<duckdb::CreateScalarFunctionInfo> GetExtractFromCIGARFunction();
+        static std::vector<duckdb::unique_ptr<duckdb::CreateScalarFunctionInfo>> GetSamFunctions();
+    };
+
+} // namespace wtt01

exon/include/exon_extension.hpp

@@ -0,0 +1,13 @@
+#pragma once
+
+#include "duckdb.hpp"
+
+namespace duckdb {
+
+class ExonExtension : public Extension {
+public:
+	void Load(DuckDB &db) override;
+	std::string Name() override;
+};
+
+} // namespace duckdb

exon/include/rust.hpp

@@ -0,0 +1,65 @@
+#include <cstdarg>
+#include <cstdint>
+#include <cstdlib>
+#include <ostream>
+#include <new>
+
+struct ReaderResult {
+  const char *error;
+};
+
+struct ReplacementScanResult {
+  const char *file_type;
+};
+
+struct CResult {
+  const char *value;
+  const char *error;
+};
+
+struct CExtractResponse {
+  uintptr_t sequence_start;
+  uintptr_t sequence_len;
+  const char *extracted_sequence;
+  const char *error;
+};
+
+extern "C" {
+
+ReaderResult new_reader(ArrowArrayStream *stream_ptr,
+                        const char *uri,
+                        uintptr_t batch_size,
+                        const char *compression,
+                        const char *file_format);
+
+ReplacementScanResult replacement_scan(const char *uri);
+
+bool is_segmented(uint16_t flag);
+
+bool is_unmapped(uint16_t flag);
+
+bool is_properly_aligned(uint16_t flag);
+
+bool is_mate_unmapped(uint16_t flag);
+
+bool is_reverse_complemented(uint16_t flag);
+
+bool is_mate_reverse_complemented(uint16_t flag);
+
+bool is_first_segment(uint16_t flag);
+
+bool is_last_segment(uint16_t flag);
+
+bool is_secondary(uint16_t flag);
+
+bool is_quality_control_failed(uint16_t flag);
+
+bool is_duplicate(uint16_t flag);
+
+bool is_supplementary(uint16_t flag);
+
+CResult parse_cigar(const char *cigar);
+
+CExtractResponse extract_from_cigar(const char *sequence_str, const char *cigar_str);
+
+} // extern "C"

exon/src/CMakeLists.txt

@@ -0,0 +1,5 @@
+add_subdirectory(exon)
+
+set(EXTENSION_SOURCES
+    ${EXTENSION_SOURCES} ${CMAKE_CURRENT_SOURCE_DIR}/exon_extension.cpp
+    PARENT_SCOPE)

exon/src/exon/CMakeLists.txt

@@ -0,0 +1,6 @@
+add_subdirectory(sam_functions)
+
+set(EXTENSION_SOURCES
+        ${EXTENSION_SOURCES}
+        PARENT_SCOPE
+)

exon/src/exon/sam_functions/CMakeLists.txt

@@ -0,0 +1,5 @@
+set(EXTENSION_SOURCES
+        ${EXTENSION_SOURCES}
+        ${CMAKE_CURRENT_SOURCE_DIR}/module.cpp
+        PARENT_SCOPE
+)