配置了cmake和调试环境

.gitignore

@@ -32,3 +32,5 @@
 *.out
 *.app
 
+lib/
+build/

.vscode/launch.json

@@ -0,0 +1,20 @@
+{
+    // 使用 IntelliSense 了解相关属性。 
+    // 悬停以查看现有属性的描述。
+    // 欲了解更多信息，请访问: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "picard_cpp",
+            "preLaunchTask": "BuildDebug",
+            // "preLaunchTask": "BuildRelease",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceRoot}/build/bin/picard_cpp",
+            "args": [
+                "MarkDuplicates"
+            ],
+            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "files.associations": {
+        "cstring": "cpp"
+    }
+}

.vscode/tasks.json

@@ -0,0 +1,27 @@
+{
+    // See https://go.microsoft.com/fwlink/?LinkId=733558
+    // for the documentation about the tasks.json format
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "BuildDebug",
+            "type": "shell",
+            "command": "cd build; cmake .. -DCMAKE_BUILD_TYPE=Debug; make -j 8",
+            "problemMatcher": [],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            }
+        },
+        {
+            "label": "BuildRelease",
+            "type": "shell",
+            "command": "cd build; cmake .. -DCMAKE_BUILD_TYPE=Release; make -j 8",
+            "problemMatcher": [],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            }
+        }
+    ]
+}

CMakeLists.txt

@@ -0,0 +1,3 @@
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+project(picard_cpp)
+ADD_SUBDIRECTORY(src)

src/CMakeLists.txt

@@ -0,0 +1,35 @@
+# 生成程序的位置
+SET(EXECUTABLE_OUTPUT_PATH "${PROJECT_BINARY_DIR}/bin")
+
+# 源码目录
+AUX_SOURCE_DIRECTORY(${PROJECT_SOURCE_DIR}/src MAIN_SRC)
+# AUX_SOURCE_DIRECTORY(${PROJECT_SOURCE_DIR}/src/common COMMON)
+AUX_SOURCE_DIRECTORY(${PROJECT_SOURCE_DIR}/src/sam SAM_SRC)
+AUX_SOURCE_DIRECTORY(${PROJECT_SOURCE_DIR}/src/sam/markdups SAM_MARKDUPS_SRC)
+
+# 头文件目录
+INCLUDE_DIRECTORIES("${PROJECT_SOURCE_DIR}/src")
+INCLUDE_DIRECTORIES("${PROJECT_SOURCE_DIR}/lib")
+INCLUDE_DIRECTORIES("${PROJECT_SOURCE_DIR}/lib/htslib")
+
+# 链接库位置
+LINK_DIRECTORIES("${PROJECT_SOURCE_DIR}/lib/htslib")
+
+# 编译生成的程序名称
+set(PG_NAME "picard_cpp")
+
+# 为程序添加依赖关系
+ADD_EXECUTABLE(${PG_NAME} ${MAIN_SRC} ${SAM_SRC} ${SAM_MARKDUPS_SRC})
+
+# 链接库
+TARGET_LINK_LIBRARIES(${PG_NAME} libhts.a)
+
+# 检测系统是否包含必需的库
+find_package(Threads REQUIRED)
+if(THREADS_HAVE_PTHREAD_ARG)
+    set_property(TARGET ${PG_NAME} PROPERTY COMPILE_OPTIONS "-pthread")
+    set_property(TARGET ${PG_NAME} PROPERTY INTERFACE_COMPILE_OPTIONS "-pthread")
+endif()
+if(CMAKE_THREAD_LIBS_INIT)
+    TARGET_LINK_LIBRARIES(${PG_NAME} "${CMAKE_THREAD_LIBS_INIT}")
+endif()

src/main.cpp

@@ -0,0 +1,60 @@
+#include <cstdio>
+#include <cstring>
+#include <htslib/sam.h>
+#include "module.h"
+
+/* 版本信息 */
+const char *version() 
+{
+    return PICARD_CPP_VERSION;
+}
+
+/* 使用说明 */
+static void usage(FILE *fp)
+{
+    fprintf(fp,
+            "\n"
+            "Program: picard_cpp (A cpp implementation for picard.)\n"
+            "Version: %s \n\n",
+            version());
+    fprintf(fp,
+            "Usage: picard_cpp <command> [options]\n"
+            "\n"
+            "Commands:\n"
+            "   MarkDuplicates        mark duplicates for bam file.\n"
+            "\n");
+}
+
+int main(int argc, char *argv[])
+{
+
+    if (argc < 2)
+    {
+        usage(stderr);
+        return 1;
+    }
+
+    if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0)
+    {
+        if (argc == 2)
+        {
+            usage(stdout);
+            return 0;
+        }
+        argv++;
+        argc = 2;
+    }
+
+    int ret = -1;
+
+    if (strcmp(argv[1], "MarkDuplicates") == 0)
+        ret = MarkDuplicates(argc - 1, argv + 1);
+    else
+    {
+        fprintf(stderr, "\n[Error]: unrecognized command '%s'\n\n", argv[1]);
+        usage(stdout);
+        return 1;
+    }
+
+    return ret;
+}

src/module.h

@@ -0,0 +1,16 @@
+/*
+     Description: picard中各种方法模块函数的前向声明
+
+     Copyright : All right reserved by NCIC.ICT
+
+     Author : Zhang Zhonghai
+     Date : 2023/10/23
+*/
+#ifndef MODULE_H_
+#define MODULE_H_
+
+#define PICARD_CPP_VERSION "v0.1"
+
+int MarkDuplicates(int argc, char *argv[]);
+
+#endif

src/sam/markdups/markdups.cpp

@@ -0,0 +1,26 @@
+/*
+Description: 标记bam文件中的冗余信息
+
+Copyright : All right reserved by ICT
+
+Author : Zhang Zhonghai
+Date : 2023/10/23
+*/
+
+#include <iostream>
+
+using namespace std;
+
+/*
+ * mark duplicate 入口
+ */
+int MarkDuplicates(int argc, char *argv[])
+{
+    cout << argc << endl;
+    for (int i = 0; i < argc; ++i) {
+        cout << argv[i] << '\t';
+    }
+    cout << endl;
+
+    return 0;
+}