org.utgenome.format.bed
Class BED2Silk

java.lang.Object
  org.utgenome.format.bed.BED2Silk

public class BED2Silk
extends Object

Converting BED into Silk format.

Note that BED is a 0-based gene data format, while UTGB uses 1-based [start, end) interval representation. To fill the gap between BED and UTGB, BED2Silk translates BED's 0-based entries into 1-based ones.

Author:

yoshimura

Nested Class Summary

static class	BED2Silk.BEDHeaderAttribute
static class	BED2Silk.BEDHeaderDescription

Constructor Summary

BED2Silk(File bedFile)

BED2Silk(Reader bedFile)

Method Summary

void	close()
String	toSilk()
void	toSilk(PrintWriter pout)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BED2Silk

public BED2Silk(File bedFile)
         throws IOException

Throws:

IOException

BED2Silk

public BED2Silk(Reader bedFile)
         throws IOException

Parameters:

bedFile -

Throws:

IOException

Method Detail

close

public void close()
           throws IOException

Throws:

IOException

toSilk

public void toSilk(PrintWriter pout)
            throws IOException,
                   UTGBException

Parameters:

out -

Throws:

IOException

UTGBShellException

UTGBException

toSilk

public String toSilk()
              throws IOException,
                     UTGBException

Throws:

IOException

UTGBException