{
    // 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": [        
        {
            "type": "java",
            "name": "BaseRecalibrator",
            "request": "launch",
            // "mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
            "mainClass": "org.broadinstitute.gatk.engine.ProtectedCLGATK",
            "projectName": "gatk-tools-protected",
            //"classPaths": [
            //    "${workspaceFolder}/target/excutable/GenomeAnalysisTK.jar",
            //    "${workspaceFolder}/target/excutable/lib/*"
            //],
            //"classPaths": [
            //    "${workspaceFolder}/protected/gatk-tools-protected/target/classes/",
            //    "${workspaceFolder}/public/gatk-engine/target/classes/",
            //],
            //"vmArgs": "-verbose:class",
            
            "args": [
                "-T", "BaseRecalibrator",
                "-R",
                "~/reference/bwa/human_g1k_v37_decoy.fasta",
                "-knownSites",
                "~/data/reference/hg19/vcfs/dbsnp_138.b37.vcf",
                "-knownSites",
                "~/data/reference/hg19/vcfs/1000G_phase1.indels.b37.vcf",
                "-I",
                //"~/data/fastdup-mini-md.bam",
                //"~/data/f1kw.sam",
                //"~/data/ft1kw.sam",
                //"~/data/difft1kw.sam",
                //"~/data/diff.sam",
                //"~/data/diff2kw.sam",
                //"~/data1/x.bam",
                //"~/data1/y.bam",
                "~/data/z.bam",
                //"~/data/z-3.sam",
                //"~/data/z-1.sam",
                "-o",
                // "./output/out-bqsr.table",
                //"./output/x.table",
                //"./output/y.table",
                //"./output/z.table",
                //"./output/z-3.table",
                "./output/f-1.table",
                // "--enable-baq",
            ]
        },
        {
            "type": "java",
            "name": "ApplyBQSR",
            "request": "launch",
            "mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
            "projectName": "gatk",
            "args": [
                "ApplyBQSR",
                "-R",
                "~/reference/bwa/human_g1k_v37_decoy.fasta",
                "-I",
                "~/data1/x.bam",
                //"~/data/z.bam",
                //"~/data/ft1kw.sam",
                "-bqsr",
                "./output/f-1.table",
                "-O",
                "./output/f-1.sam",
            ]
        }
    ]
}