Ejemplo n.º 1
0
 @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);
 }
Ejemplo n.º 2
0
 @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);
 }
Ejemplo n.º 3
0
 @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);
 }
Ejemplo n.º 4
0
 @Override
 public void printOptions(java.io.PrintStream out) {
   out.println(" -k (uri/file) knownGene source. Required. Default: " + ucscKnownGene);
   super.printOptions(out);
 }
Ejemplo n.º 5
0
 @Override
 public void printOptions(PrintStream out) {
   out.println(" -D (dir) berkeleydb home. REQUIRED.");
   out.println(" -M (max depth) default:3");
   super.printOptions(out);
 }
Ejemplo n.º 6
0
 @Override
 public void printOptions(java.io.PrintStream out) {
   out.println("-p (chrom:pos) region");
   super.printOptions(out);
 }