org.broadinstitute.hellbender.utils.io

Class BlockCompressedIntervalStream.Writer<F extends htsjdk.tribble.Feature>

java.lang.Object

org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer<F>

All Implemented Interfaces:

FeatureSink<F>

Enclosing class:

BlockCompressedIntervalStream

public static class BlockCompressedIntervalStream.Writer<F extends htsjdk.tribble.Feature>
extends java.lang.Object
implements FeatureSink<F>

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_COMPRESSION_LEVEL

Constructor Summary

Constructors

Constructor and Description
Writer(GATKPath path, FeaturesHeader header, BlockCompressedIntervalStream.WriteFunc<F> writeFunc)
Writer(GATKPath path, FeaturesHeader header, BlockCompressedIntervalStream.WriteFunc<F> writeFunc, int compressionLevel)
Writer(java.lang.String streamSource, java.io.OutputStream os, FeaturesHeader header, BlockCompressedIntervalStream.WriteFunc<F> writeFunc)

Method Summary

Modifier and Type	Method and Description
void	close()
int	getContigIndex(java.lang.String contigName)
int	getSampleIndex(java.lang.String sampleName)
java.io.DataOutputStream	getStream()
void	write(F feature)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_COMPRESSION_LEVEL

public static final int DEFAULT_COMPRESSION_LEVEL

See Also:

Constant Field Values

Constructor Detail

Writer

public Writer(GATKPath path,
              FeaturesHeader header,
              BlockCompressedIntervalStream.WriteFunc<F> writeFunc)

Writer

public Writer(GATKPath path,
              FeaturesHeader header,
              BlockCompressedIntervalStream.WriteFunc<F> writeFunc,
              int compressionLevel)

Writer

public Writer(java.lang.String streamSource,
              java.io.OutputStream os,
              FeaturesHeader header,
              BlockCompressedIntervalStream.WriteFunc<F> writeFunc)

Method Detail

getStream

public java.io.DataOutputStream getStream()

getSampleIndex

public int getSampleIndex(java.lang.String sampleName)

getContigIndex

public int getContigIndex(java.lang.String contigName)

write

public void write(F feature)

Specified by:

write in interface FeatureSink<F extends htsjdk.tribble.Feature>

close

public void close()

Specified by:

close in interface FeatureSink<F extends htsjdk.tribble.Feature>