hyb-align/.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": "${workspaceRoot}/hybalign",
            "args": [
                "mem",
                "-t",
                "128",
                "-K", "800000000",
                "-M",
                "-R",
                "'@RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa'",
                // "/home/zzh/work/bioinfo/hyb-align/index/human_g1k_v37_decoy.fasta",
                "~/data/reference/hyb/human_g1k_v37_decoy.fasta",
                //"./b1.fq", "./b2.fq",
                //"~/data/dataset/real/D1/n1.fq", "~/data/dataset/real/D1/n2.fq",
                //"~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_1.fq",
                //"~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_2.fq",
                //"~/data/dataset/real/D3/n1.fq",
                //"~/data/dataset/real/D3/n2.fq",
                // "~/data/dataset/real/D2/n1.fq.gz", "~/data/dataset/real/D2/n2.fq.gz",
                "~/data/dataset/D2/n1.fq.gz", "~/data/dataset/D2/n2.fq.gz",
                //"~/data/dataset/real/D3/1w1.fq", "~/data/dataset/real/D3/1w2.fq",
                "-o",
                "/dev/null",
                // "-g",
            ],
            "cwd": "${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": "${workspaceRoot}/hybalign",
            "args": [
                "index",
                "~/data/reference/human_g1k_v37_decoy.fasta"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "buildkmer",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/hybalign",
            "args": [
                "buildkmer",
                "~/data/reference/human_g1k_v37_decoy.fasta.256.64.fmt",
                "~/data/reference/human_g1k_v37_decoy.fasta.kmer"
            ],
            "cwd": "${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": "${workspaceRoot}/hybalign",
            "args": [
                "shm",
                "-Z",
                "~/data1/fmt_ref/human_g1k_v37_decoy.fasta"
            ],
            "cwd": "${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": "${workspaceRoot}/hybalign",
            "args": [
                "pac2bref",
                "~/data1/fmt_ref/human_g1k_v37_decoy.fasta"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "build hybrid index",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/hybalign",
            "args": [
                "bwt2hyb",
                "-t",
                "1",
                "./index/human_g1k_v37_decoy.fasta"
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
        {
            "name": "fa2pac",
            "preLaunchTask": "Build",
            "type": "cppdbg",
            "request": "launch",
            "program": "${workspaceRoot}/hybalign",
            "args": [
                "fa2pac",
                "-f",
                "~/data/fmt_ref/human_g1k_v37_decoy.fasta",
            ],
            "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
        },
    ]
}