use of cz1.util.ArgsEngine in project polyGembler by c-zhou.
the class ZipDataCollection 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("-i", "--vcf", true);
myArgsEngine.add("-s", "--id", true);
myArgsEngine.add("-o", "--prefix", true);
myArgsEngine.parse(args);
}
if (myArgsEngine.getBoolean("-i")) {
vcf_in = myArgsEngine.getString("-i");
} else {
printUsage();
throw new IllegalArgumentException("Please specify your VCF file.");
}
if (myArgsEngine.getBoolean("-s")) {
id = myArgsEngine.getString("-s");
} else {
id = new File(vcf_in).getName().replaceAll(".vcf.gz$", "").replaceAll(".vcf$", "");
}
if (myArgsEngine.getBoolean("-o")) {
out_file = myArgsEngine.getString("-o");
} else {
out_file = new File(vcf_in).getParent();
}
}
use of cz1.util.ArgsEngine in project polyGembler by c-zhou.
the class GenomeAssemblyTiling 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("-d", "--rdot-plot", true);
myArgsEngine.add("-s", "--size", true);
myArgsEngine.add("-f", "--rf", true);
myArgsEngine.add("-r", "--reference", true);
myArgsEngine.add("-q", "--query", true);
myArgsEngine.add("-l", "--colinear-thres", true);
myArgsEngine.add("-t", "--threads", true);
myArgsEngine.add("-o", "--out-prefix", true);
myArgsEngine.parse(args);
}
if (myArgsEngine.getBoolean("-d")) {
rdot_file = myArgsEngine.getString("-d");
} else {
printUsage();
throw new IllegalArgumentException("Please specify the location of the Rdor-plot files.");
}
if (myArgsEngine.getBoolean("-s")) {
size_file = myArgsEngine.getString("-s");
} else {
printUsage();
throw new IllegalArgumentException("Please specify the chromosome/scaffold/contig size file.");
}
if (myArgsEngine.getBoolean("-f")) {
rf_file = myArgsEngine.getString("-f");
} else {
printUsage();
throw new IllegalArgumentException("Please specify the recombination frequency file.");
}
if (myArgsEngine.getBoolean("-r")) {
refAssembly = myArgsEngine.getString("-r");
} else {
printUsage();
throw new IllegalArgumentException("Please specify the reference id.");
}
if (myArgsEngine.getBoolean("-q")) {
qryAssembly = myArgsEngine.getString("-q");
} else {
printUsage();
throw new IllegalArgumentException("Please specify the query id.");
}
if (myArgsEngine.getBoolean("-l")) {
cl_thres = Double.parseDouble(myArgsEngine.getString("-l"));
}
if (myArgsEngine.getBoolean("-o")) {
out_prefix = myArgsEngine.getString("-o");
}
if (myArgsEngine.getBoolean("-t")) {
THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
}
}
use of cz1.util.ArgsEngine in project polyGembler by c-zhou.
the class AssemblyError 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("-ex", "--experiment-id", true);
myArgsEngine.add("-i", "--hap-file", true);
myArgsEngine.add("-o", "--prefix", true);
myArgsEngine.add("-f", "--parent", true);
myArgsEngine.add("-p", "--ploidy", true);
myArgsEngine.add("-nb", "--best", true);
myArgsEngine.add("-t", "--threads", true);
myArgsEngine.add("-phi", "--skew-phi", true);
myArgsEngine.add("-nd", "--drop", true);
myArgsEngine.parse(args);
}
if (myArgsEngine.getBoolean("-i")) {
in_haps = myArgsEngine.getString("-i");
} else {
printUsage();
throw new IllegalArgumentException("Please specify your input zip file.");
}
if (myArgsEngine.getBoolean("-o")) {
out_prefix = myArgsEngine.getString("-o");
} else {
printUsage();
throw new IllegalArgumentException("Please specify your output file prefix.");
}
if (myArgsEngine.getBoolean("-ex")) {
expr_id = myArgsEngine.getString("-ex");
} else {
expr_id = guessExperimentId();
myLogger.warn("No experiment prefix provided, I guess it's " + expr_id + ". Please\n" + "specify it with -ex/--experiment-id option if it's incorrect.");
}
if (myArgsEngine.getBoolean("-f")) {
founder_haps = myArgsEngine.getString("-f").split(":");
} else {
printUsage();
throw new IllegalArgumentException("Please specify the parent samples (seperated by a \":\").");
}
if (myArgsEngine.getBoolean("-p")) {
int ploidy = Integer.parseInt(myArgsEngine.getString("-p"));
Constants.ploidy(ploidy);
Constants._haplotype_z = ploidy * 2;
probs_uniform = new double[ploidy * 2];
Arrays.fill(probs_uniform, .5 / ploidy);
}
if (myArgsEngine.getBoolean("-nb")) {
best_n = Integer.parseInt(myArgsEngine.getString("-nb"));
}
if (myArgsEngine.getBoolean("-t")) {
THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
}
if (myArgsEngine.getBoolean("-phi")) {
skew_phi = Integer.parseInt(myArgsEngine.getString("-phi"));
}
if (myArgsEngine.getBoolean("-nd")) {
drop_thres = Integer.parseInt(myArgsEngine.getString("-nd"));
}
}
use of cz1.util.ArgsEngine in project polyGembler by c-zhou.
the class DataPreparation 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", "--vcf", true);
myArgsEngine.add("-s", "--id", true);
myArgsEngine.add("-l", "--min-depth", true);
myArgsEngine.add("-p", "--ploidy", true);
myArgsEngine.add("-u", "--max-depth", true);
myArgsEngine.add("-q", "--min-qual", true);
myArgsEngine.add("-f", "--min-maf", true);
myArgsEngine.add("-m", "--max-missing", true);
myArgsEngine.add("-o", "--prefix", true);
myArgsEngine.parse(args);
}
if (myArgsEngine.getBoolean("-i")) {
vcf_in = myArgsEngine.getString("-i");
} else {
printUsage();
throw new IllegalArgumentException("Please specify your VCF file.");
}
if (myArgsEngine.getBoolean("-s")) {
id = myArgsEngine.getString("-s");
} else {
id = new File(vcf_in).getName().replaceAll(".vcf.gz$", "").replaceAll(".vcf$", "") + ".recode";
}
if (myArgsEngine.getBoolean("-p")) {
ploidy = Integer.parseInt(myArgsEngine.getString("-p"));
}
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("-f")) {
min_maf = Double.parseDouble(myArgsEngine.getString("-f"));
}
if (myArgsEngine.getBoolean("-m")) {
max_missing = Double.parseDouble(myArgsEngine.getString("-m"));
}
if (myArgsEngine.getBoolean("-o")) {
out_file = myArgsEngine.getString("-o");
} else {
out_file = new File(vcf_in).getParent();
if (out_file == null)
out_file = "./";
}
}
use of cz1.util.ArgsEngine in project polyGembler by c-zhou.
the class SAMtools method setParameters.
@Override
public void setParameters(String[] args) {
// TODO Auto-generated method stub
if (myArgsEngine == null) {
myArgsEngine = new ArgsEngine();
myArgsEngine.add("-i", "--sam-file", true);
myArgsEngine.add("-o", "--prefix", true);
myArgsEngine.parse(args);
}
if (myArgsEngine.getBoolean("-i")) {
mySamFile = myArgsEngine.getString("-i");
} else {
printUsage();
throw new IllegalArgumentException("Please specify your SAM/BAM file.");
}
if (myArgsEngine.getBoolean("-o")) {
myOutput = myArgsEngine.getString("-o");
} else {
printUsage();
throw new IllegalArgumentException("Please specify your output file.");
}
}
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