org.utgenome.format.sam
Class SAM2SilkReader

java.lang.Object
  java.io.Reader
      org.utgenome.format.FormatConversionReader
          org.utgenome.format.sam.SAM2SilkReader

All Implemented Interfaces:

Closeable, Readable

public class SAM2SilkReader
extends FormatConversionReader

Reader for converting SAM into Silk

Author:

leo

Nested Class Summary

Nested classes/interfaces inherited from class org.utgenome.format.FormatConversionReader

FormatConversionReader.PipeConsumer

Field Summary

Fields inherited from class java.io.Reader

lock

Constructor Summary

SAM2SilkReader(InputStream input)

SAM2SilkReader(Reader input)

Method Summary

static SAMRead	convertToSAMRead(net.sf.samtools.SAMRecord record) convert a SAMRecord into a SAMRead, which can be used in GWT code.
static SAMReadLight	convertToSAMReadLight(net.sf.samtools.SAMRecord record) convert a SAMRecord into a SAMRead, which can be used in GWT code.
static String	toSilk(net.sf.samtools.SAMRecord rec) Convert an input SAMRecord into Silk format
static void	toSilk(net.sf.samtools.SAMRecord rec, org.xerial.silk.SilkWriter w) Convert an input SAMRecord into Silk format by using a given SilkWriter

Methods inherited from class org.utgenome.format.FormatConversionReader

close, read

Methods inherited from class java.io.Reader

mark, markSupported, read, read, read, ready, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

SAM2SilkReader

public SAM2SilkReader(InputStream input)
               throws IOException

Throws:

IOException

SAM2SilkReader

public SAM2SilkReader(Reader input)
               throws IOException

Throws:

IOException

Method Detail

convertToSAMRead

public static SAMRead convertToSAMRead(net.sf.samtools.SAMRecord record)

convert a SAMRecord into a SAMRead, which can be used in GWT code.

Parameters:

record -

Returns:

convertToSAMReadLight

public static SAMReadLight convertToSAMReadLight(net.sf.samtools.SAMRecord record)

convert a SAMRecord into a SAMRead, which can be used in GWT code.

Parameters:

record -

Returns:

toSilk

public static void toSilk(net.sf.samtools.SAMRecord rec,
                          org.xerial.silk.SilkWriter w)

Convert an input SAMRecord into Silk format by using a given SilkWriter

Parameters:

rec -

w -

toSilk

public static String toSilk(net.sf.samtools.SAMRecord rec)

Convert an input SAMRecord into Silk format

Parameters:

rec -

Returns: