Examples with ArgsEngine cz1.util.ArgsEngine used on opensource projects

Example 11 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class PopulationSimulator method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (args.length == 0) {
        printUsage();
        throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-r", "--reference", true);
        myArgsEngine.add("-n", "--pop-size", true);
        myArgsEngine.add("-p", "--ploidy", true);
        myArgsEngine.add("-c", "--centimorgan", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-s", "--run-id", true);
        myArgsEngine.add("-o", "--prefix", true);
        myArgsEngine.parse(args);
    }
    String reference, id = "Sc1", output = "./";
    int f1 = 94, ploidy = 2;
    double cM = -1.0;
    if (myArgsEngine.getBoolean("-r")) {
        reference = myArgsEngine.getString("-r");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the reference FASTA file.");
    }
    if (myArgsEngine.getBoolean("-n")) {
        f1 = Integer.parseInt(myArgsEngine.getString("-n")) - 2;
    }
    if (myArgsEngine.getBoolean("-p")) {
        ploidy = Integer.parseInt(myArgsEngine.getString("-p"));
    }
    if (myArgsEngine.getBoolean("-c")) {
        cM = Double.parseDouble(myArgsEngine.getString("-c"));
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-s")) {
        id = myArgsEngine.getString("-s");
    }
    if (myArgsEngine.getBoolean("-o")) {
        output = myArgsEngine.getString("-o");
    }
    pop = new Population(reference, f1, ploidy, cM, id, output);
}

Example 12 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class BAMstats method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-i1", "--in-bam1", true);
        myArgsEngine.add("-i2", "--in-bam2", true);
        myArgsEngine.add("-o", "--out", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i1")) {
        this.bam_in1 = myArgsEngine.getString("-i1");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the input BAM file.");
    }
    if (myArgsEngine.getBoolean("-i2")) {
        this.bam_in2 = myArgsEngine.getString("-i2");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the input BAM file.");
    }
    if (myArgsEngine.getBoolean("-o")) {
        this.out = myArgsEngine.getString("-o");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the output file.");
    }
}

Example 13 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class TenXSamtools method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (args.length == 0) {
        printUsage();
        throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    switch(args[0].toUpperCase()) {
        case "SORT":
            this.task = Task.sort;
            break;
        default:
            printUsage();
            throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    String[] args2 = new String[args.length - 1];
    System.arraycopy(args, 1, args2, 0, args2.length);
    switch(this.task) {
        case sort:
            if (myArgsEngine == null) {
                myArgsEngine = new ArgsEngine();
                myArgsEngine.add("-i", "--in-bam", true);
                myArgsEngine.add("-b", "--barcode", false);
                myArgsEngine.add("-n", "--name", false);
                myArgsEngine.add("-s", "--batch-size", true);
                myArgsEngine.add("-t", "--threads", true);
                myArgsEngine.add("-o", "--out-bam", true);
                myArgsEngine.parse(args2);
            }
            if (myArgsEngine.getBoolean("-i")) {
                this.bam_in = myArgsEngine.getString("-i");
            } else {
                printUsage();
                throw new IllegalArgumentException("Please specify the input BAM file.");
            }
            if (myArgsEngine.getBoolean("-b") && myArgsEngine.getBoolean("-n")) {
                printUsage();
                throw new IllegalArgumentException("Options -b and -n are exculsive!!!");
            }
            if (myArgsEngine.getBoolean("-b")) {
                this.sort_order = Order.barcode;
                comprator = new Comparator<SAMRecord>() {

                    @Override
                    public int compare(SAMRecord record1, SAMRecord record2) {
                        // TODO Auto-generated method stub
                        if (record1 == null && record2 == null)
                            return 0;
                        if (record1 == null)
                            return 1;
                        if (record2 == null)
                            return -1;
                        String bx1 = record1.getStringAttribute("BX"), bx2 = record2.getStringAttribute("BX");
                        if (bx1 == null && bx2 == null)
                            return compareSAMRecord(record1, record2);
                        // none barcode record to the end
                        if (bx1 == null)
                            return 1;
                        if (bx2 == null)
                            return -1;
                        int diff = bx1.compareTo(bx2);
                        return diff == 0 ? compareSAMRecord(record1, record2) : diff;
                    }
                };
            }
            if (myArgsEngine.getBoolean("-n")) {
                this.sort_order = Order.queryname;
                comprator = new Comparator<SAMRecord>() {

                    @Override
                    public int compare(SAMRecord record1, SAMRecord record2) {
                        // TODO Auto-generated method stub
                        if (record1 == null && record2 == null)
                            return 0;
                        if (record1 == null)
                            return 1;
                        if (record2 == null)
                            return -1;
                        if (record1.getReadName().compareTo(record2.getReadName()) == 0)
                            return compareSAMRecord(record1, record2);
                        return record1.getReadName().compareTo(record2.getReadName());
                    }
                };
            }
            if (myArgsEngine.getBoolean("-s")) {
                this.batch_size = Integer.parseInt(myArgsEngine.getString("-s"));
            }
            if (myArgsEngine.getBoolean("-t")) {
                this.THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
            }
            if (myArgsEngine.getBoolean("-o")) {
                this.bam_out = myArgsEngine.getString("-o");
            } else {
                printUsage();
                throw new IllegalArgumentException("Please specify the output BAM file.");
            }
            break;
        default:
            throw new RuntimeException("!!!");
    }
}

Example 14 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class TenxMoleculeTools method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-i", "--in", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-o", "--out", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i")) {
        this.file_in = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the input file.");
    }
    if (myArgsEngine.getBoolean("-t")) {
        this.THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-o")) {
        this.file_out = myArgsEngine.getString("-o");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the output file.");
    }
}

Example 15 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class Gembler method setParameters.

@Override
public void setParameters(String[] args) {
    if (args.length == 0) {
        printUsage();
        throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-i", "--input-vcf", true);
        myArgsEngine.add("-a", "--input-assembly", true);
        myArgsEngine.add("-o", "--prefix", true);
        myArgsEngine.add("-x", "--max-iter", true);
        myArgsEngine.add("-p", "--ploidy", true);
        myArgsEngine.add("-f", "--parent", true);
        myArgsEngine.add("-G", "--genotype", false);
        myArgsEngine.add("-D", "--allele-depth", false);
        myArgsEngine.add("-L", "--genotype-likelihood", false);
        myArgsEngine.add("-b", "--segmental-kmeans", false);
        myArgsEngine.add("-S", "--random-seed", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-l", "--min-depth", true);
        myArgsEngine.add("-u", "--max-depth", true);
        myArgsEngine.add("-q", "--min-qual", true);
        myArgsEngine.add("-mf", "--min-maf", true);
        myArgsEngine.add("-mm", "--max-missing", true);
        myArgsEngine.add("-c", "--min-snp-count", true);
        myArgsEngine.add("-r", "--repeat", true);
        myArgsEngine.add("-rr", "--refinement-round", true);
        myArgsEngine.add("-nb", "--best", true);
        myArgsEngine.add("-phi", "--skew-phi", true);
        myArgsEngine.add("-nd", "--drop", true);
        myArgsEngine.add("-rlib", "--R-external-libs", true);
        myArgsEngine.add("-frac", "--frac-thresold", true);
        myArgsEngine.add("-gz", "--genome-size", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i")) {
        in_vcf = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify your input VCF file.");
    }
    if (myArgsEngine.getBoolean("-a")) {
        assembly_file = myArgsEngine.getString("-a");
    }
    if (myArgsEngine.getBoolean("-o")) {
        out_prefix = myArgsEngine.getString("-o");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify your output file prefix.");
    }
    if (myArgsEngine.getBoolean("-x")) {
        max_iter = Integer.parseInt(myArgsEngine.getString("-x"));
    }
    if (myArgsEngine.getBoolean("-p")) {
        Constants.ploidy(Integer.parseInt(myArgsEngine.getString("-p")));
    }
    if (myArgsEngine.getBoolean("-f")) {
        Constants._founder_haps = myArgsEngine.getString("-f");
        founder_haps = Constants._founder_haps.split(":");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the parent samples (seperated by a \":\").");
    }
    int c = 0;
    if (myArgsEngine.getBoolean("-G")) {
        field = Field.GT;
        c++;
    }
    if (myArgsEngine.getBoolean("-D")) {
        field = Field.AD;
        c++;
    }
    if (myArgsEngine.getBoolean("-L")) {
        field = Field.PL;
        c++;
    }
    if (c > 1)
        throw new IllegalArgumentException("Options -G/--genotype, " + "-D/--allele-depth, and -L/--genotype-likelihood " + "are exclusive!!!");
    if (myArgsEngine.getBoolean("-b")) {
        vbt = true;
        throw new RuntimeException("Viterbi training not supported yet!!!");
    }
    if (myArgsEngine.getBoolean("-S")) {
        Constants.seed = Long.parseLong(myArgsEngine.getString("-S"));
        Constants.setRandomGenerator();
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-l")) {
        min_depth = Integer.parseInt(myArgsEngine.getString("-l"));
    }
    if (myArgsEngine.getBoolean("-u")) {
        max_depth = Integer.parseInt(myArgsEngine.getString("-u"));
    }
    if (myArgsEngine.getBoolean("-q")) {
        min_qual = Integer.parseInt(myArgsEngine.getString("-q"));
    }
    if (myArgsEngine.getBoolean("-mf")) {
        min_maf = Double.parseDouble(myArgsEngine.getString("-mf"));
    }
    if (myArgsEngine.getBoolean("-mm")) {
        max_missing = Double.parseDouble(myArgsEngine.getString("-mm"));
    }
    if (myArgsEngine.getBoolean("-c")) {
        min_snpc = Integer.parseInt(myArgsEngine.getString("-c"));
    }
    if (myArgsEngine.getBoolean("-r")) {
        String[] rs = myArgsEngine.getString("-r").split(",");
        if (rs.length != 3)
            throw new IllegalArgumentException("Option -r/--repeat should " + "be 3 integers seperated by \",\".");
        for (int i = 0; i < 3; i++) repeat[i] = Integer.parseInt(rs[i]);
    }
    if (myArgsEngine.getBoolean("-rr")) {
        refine_round = Integer.parseInt(myArgsEngine.getString("-rr"));
    }
    if (myArgsEngine.getBoolean("-nb")) {
        nB = Integer.parseInt(myArgsEngine.getString("-nb"));
    }
    if (myArgsEngine.getBoolean("-phi")) {
        phi = Double.parseDouble(myArgsEngine.getString("-phi"));
    }
    if (myArgsEngine.getBoolean("-nd")) {
        drop = Integer.parseInt(myArgsEngine.getString("-nd"));
    }
    if (myArgsEngine.getBoolean("-rlib")) {
        RLibPath = myArgsEngine.getString("-rlib");
    }
    if (myArgsEngine.getBoolean("-frac")) {
        frac_thresh = Double.parseDouble(myArgsEngine.getString("-frac"));
    }
    if (myArgsEngine.getBoolean("-gz")) {
        genome_size = Double.parseDouble(myArgsEngine.getString("-gz"));
    }
}