BWA-FastAlign/.vscode/launch.json

{
    // 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": "bwa-mem",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/fastalign",
            "args": [
                "mem",
                "-t",
                "32",
                "-M",
                "-R",
                "'@RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa'",
                "~/data/reference/fmt/human_g1k_v37_decoy.fasta",
                "~/data/dataset/D1/n1.fq.gz",
                "~/data/dataset/D1/n2.fq.gz",
                "-o",
                "D1-out.sam",
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "index",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/fastalign",
            "args": [
                "index",
                "./index/ref.fasta"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "buildkmer",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/fastalign",
            "args": [
                "buildkmer",
                "~/data/reference/human_g1k_v37_decoy.fasta.256.64.fmt",
                "~/data/reference/human_g1k_v37_decoy.fasta.kmer"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "share mem",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/fastalign",
            "args": [
                "shm",
                "-Z",
                "~/data1/fmt_ref/human_g1k_v37_decoy.fasta"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "pac to bref",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/fastalign",
            "args": [
                "pac2bref",
                "~/data1/fmt_ref/human_g1k_v37_decoy.fasta"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        }
    ]
}