org.broadinstitute.hellbender.utils.io

Class BlockCompressedIntervalStream.Reader<T extends htsjdk.tribble.Feature>

java.lang.Object

org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader<T>

All Implemented Interfaces:

htsjdk.tribble.FeatureReader<T>, java.io.Closeable, java.lang.AutoCloseable

Enclosing class:

BlockCompressedIntervalStream

public static final class BlockCompressedIntervalStream.Reader<T extends htsjdk.tribble.Feature>
extends java.lang.Object
implements htsjdk.tribble.FeatureReader<T>

Constructor Summary

Constructors

Constructor and Description
Reader(BlockCompressedIntervalStream.Reader<T> reader)
Reader(FeatureInput<T> inputDescriptor, htsjdk.tribble.FeatureCodec<T,BlockCompressedIntervalStream.Reader<T>> codec)
Reader(java.lang.String inputStreamName, htsjdk.samtools.seekablestream.SeekableStream ss, htsjdk.tribble.FeatureCodec<T,BlockCompressedIntervalStream.Reader<T>> codec)

Method Summary

Modifier and Type	Method and Description
void	close()
htsjdk.samtools.SAMSequenceDictionary	getDictionary()
htsjdk.tribble.FeatureCodecHeader	getFeatureCodecHeader()
java.lang.Object	getHeader()
long	getPosition()
java.util.List<java.lang.String>	getSampleNames()
java.util.List<java.lang.String>	getSequenceNames()
java.io.DataInputStream	getStream()
java.lang.String	getVersion()
boolean	hasNext()
boolean	isQueryable()
htsjdk.tribble.CloseableTribbleIterator<T>	iterator()
htsjdk.tribble.CloseableTribbleIterator<T>	query(java.lang.String chr, int start, int end)
T	readStream()
void	seekStream(long filePointer)

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.FeatureReader

query

Constructor Detail

Reader

public Reader(FeatureInput<T> inputDescriptor,
              htsjdk.tribble.FeatureCodec<T,BlockCompressedIntervalStream.Reader<T>> codec)

Reader

public Reader(BlockCompressedIntervalStream.Reader<T> reader)

Reader

public Reader(java.lang.String inputStreamName,
              htsjdk.samtools.seekablestream.SeekableStream ss,
              htsjdk.tribble.FeatureCodec<T,BlockCompressedIntervalStream.Reader<T>> codec)

Method Detail

getFeatureCodecHeader

public htsjdk.tribble.FeatureCodecHeader getFeatureCodecHeader()

getStream

public java.io.DataInputStream getStream()

getSampleNames

public java.util.List<java.lang.String> getSampleNames()

getDictionary

public htsjdk.samtools.SAMSequenceDictionary getDictionary()

getVersion

public java.lang.String getVersion()

hasNext

public boolean hasNext()

query

public htsjdk.tribble.CloseableTribbleIterator<T> query(java.lang.String chr,
                                                        int start,
                                                        int end)
                                                 throws java.io.IOException

Specified by:

query in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

Throws:

java.io.IOException

iterator

public htsjdk.tribble.CloseableTribbleIterator<T> iterator()

Specified by:

iterator in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

close

public void close()

Specified by:

close in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getSequenceNames

public java.util.List<java.lang.String> getSequenceNames()

Specified by:

getSequenceNames in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

getHeader

public java.lang.Object getHeader()

Specified by:

getHeader in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

isQueryable

public boolean isQueryable()

Specified by:

isQueryable in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

getPosition

public long getPosition()

seekStream

public void seekStream(long filePointer)

readStream

public T readStream()