htsjdk.tribble

Class TabixFeatureReader<T extends Feature,SOURCE>

java.lang.Object

htsjdk.tribble.AbstractFeatureReader<T,SOURCE>

htsjdk.tribble.TabixFeatureReader<T,SOURCE>

All Implemented Interfaces:

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

public class TabixFeatureReader<T extends Feature,SOURCE>
extends AbstractFeatureReader<T,SOURCE>

Since:

2/11/12

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.tribble.AbstractFeatureReader

AbstractFeatureReader.ComponentMethods

Field Summary

Fields inherited from class htsjdk.tribble.AbstractFeatureReader

BLOCK_COMPRESSED_EXTENSIONS, codec, header

Constructor Summary

Constructors

Constructor and Description
TabixFeatureReader(java.lang.String featureFile, AsciiFeatureCodec codec)
TabixFeatureReader(java.lang.String featureFile, java.lang.String indexFile, AsciiFeatureCodec codec)
TabixFeatureReader(java.lang.String featureFile, java.lang.String indexFile, AsciiFeatureCodec codec, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper)

Method Summary

Modifier and Type	Method and Description
void	close() Closes the reader
java.util.List<java.lang.String>	getSequenceNames() Provides the list of sequenceNames if known.
boolean	hasIndex() Whether the reader has an index or not Default implementation returns false
CloseableTribbleIterator<T>	iterator() Provides access to all the features in the reader
CloseableTribbleIterator<T>	query(java.lang.String chr, int start, int end) Return iterator over all features overlapping the given interval

Methods inherited from class htsjdk.tribble.AbstractFeatureReader

getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, hasBlockCompressedExtension, isQueryable, isTabix, setComponentMethods

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

TabixFeatureReader

public TabixFeatureReader(java.lang.String featureFile,
                          AsciiFeatureCodec codec)
                   throws java.io.IOException

Parameters:

featureFile - - path to a feature file. Can be a local file, http url, or ftp url

codec -

Throws:

java.io.IOException

TabixFeatureReader

public TabixFeatureReader(java.lang.String featureFile,
                          java.lang.String indexFile,
                          AsciiFeatureCodec codec)
                   throws java.io.IOException

Parameters:

featureFile - - path to a feature file. Can be a local file, http url, or ftp url

indexFile - - path to the index file.

codec -

Throws:

java.io.IOException

TabixFeatureReader

public TabixFeatureReader(java.lang.String featureFile,
                          java.lang.String indexFile,
                          AsciiFeatureCodec codec,
                          java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper,
                          java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexWrapper)
                   throws java.io.IOException

Parameters:

featureFile - path to a feature file. Can be a local file, http url, or ftp url

indexFile - path to the index file.

wrapper - a wrapper to apply to the byte stream from the featureResource allowing injecting features like caching and prefetching of the stream, may be null, will only be applied if featureFile is a uri representing a Path

indexWrapper - a wrapper to apply to the byte stream from the indexResource, may be null, will only be applied if indexFile is a uri representing a Path

Throws:

java.io.IOException

Method Detail

hasIndex

public boolean hasIndex()

Description copied from class: AbstractFeatureReader

Whether the reader has an index or not Default implementation returns false

Overrides:

hasIndex in class AbstractFeatureReader<T extends Feature,SOURCE>

Returns:

false

getSequenceNames

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

Description copied from interface: FeatureReader

Provides the list of sequenceNames if known. Otherwise will return an empty list.

Returns:

the list of sequenceNames if known. Otherwise will return an empty list.

query

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

Return iterator over all features overlapping the given interval

Parameters:

chr -

start -

end -

Returns:

Throws:

java.io.IOException

iterator

public CloseableTribbleIterator<T> iterator()
                                     throws java.io.IOException

Description copied from interface: FeatureReader

Provides access to all the features in the reader

Returns:

an iterator to all the features in the reader

Throws:

java.io.IOException - If there's a problem reading.

close

public void close()
           throws java.io.IOException

Description copied from interface: FeatureReader

Closes the reader

Throws:

java.io.IOException