@Override
public void printOptions(PrintStream out) {
out.println(" -n (int) number of reads. -1: all reads");
out.println(" -o (file) output file (default stdout)");
out.println(" -N (int) max records in ram (optional)");
out.println(" -b force binary for stdout (optional)");
out.println(" -T (dir) add tmp directory (optional)");
super.printOptions(out);
}
@Override
public void printOptions(java.io.PrintStream out) {
out.println(" -R (ref) fasta reference file indexed with samtools. Required.");
out.println(" -w (int: size) square size default:" + viewRect.width);
out.println(" -o (file.jpg) ouput file. Required");
out.println(" -T just list countries and exit.");
out.println(" -u (uri) URL world SVG map. Default is: " + svgMapUri);
super.printOptions(out);
}
@Override
public void printOptions(java.io.PrintStream out) {
out.println(" -t (dir) " + getMessageBundle("illegal.number.of.arguments") + " . Optional.");
out.println(" -F (fastq) Save fastq_R1 to file (default: stdout) . Optional.");
out.println(" -R (fastq) Save fastq_R2 to file (default: interlaced with forward) . Optional.");
out.println(" -r repair: insert missing read");
out.println(" -N (int) " + getMessageBundle("max.records.in.ram") + ". Optional.");
super.printOptions(out);
}
@Override
public void printOptions(java.io.PrintStream out) {
out.println(" -k (uri/file) knownGene source. Required. Default: " + ucscKnownGene);
super.printOptions(out);
}
@Override
public void printOptions(PrintStream out) {
out.println(" -D (dir) berkeleydb home. REQUIRED.");
out.println(" -M (max depth) default:3");
super.printOptions(out);
}
@Override
public void printOptions(java.io.PrintStream out) {
out.println("-p (chrom:pos) region");
super.printOptions(out);
}