@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); }