Package htsjdk.tribble

Class TribbleIndexedFeatureReader<T extends Feature,SOURCE>

java.lang.Object

htsjdk.tribble.AbstractFeatureReader<T,SOURCE>

htsjdk.tribble.TribbleIndexedFeatureReader<T,SOURCE>

All Implemented Interfaces:

FeatureReader<T>, Closeable, AutoCloseable

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

A reader for text feature files (i.e. not tabix files). This includes tribble-indexed and non-indexed files. If index both iterate() and query() methods are supported.

Note: Non-indexed files can be gzipped, but not bgzipped.

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	Description
TribbleIndexedFeatureReader(String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex)
TribbleIndexedFeatureReader(String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
TribbleIndexedFeatureReader(String featureFile, FeatureCodec<T,SOURCE> codec, Index index)
TribbleIndexedFeatureReader(String featureFile, String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex)
TribbleIndexedFeatureReader(String featureFile, String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)

Method Summary

Modifier and Type	Method	Description
void	close()	Closes the reader
List<String>	getSequenceNames()	Return the sequence (chromosome/contig) names in this file, if known.
boolean	hasIndex()	Whether the reader has an index or not Default implementation returns false
boolean	isQueryable()
CloseableTribbleIterator<T>	iterator()	Provides access to all the features in the reader
CloseableTribbleIterator<T>	query(String chr, int start, int end)	Return an iterator to iterate over features overlapping the specified interval

Methods inherited from class htsjdk.tribble.AbstractFeatureReader

getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, hasBlockCompressedExtension, 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 Details

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(String featurePath,
 FeatureCodec<T,SOURCE> codec,
 boolean requireIndex)
                            throws IOException

Parameters:

featurePath - - path to the feature file, can be a local file path, http url, or ftp url

codec - - codec to decode the features

requireIndex - - true if the reader will be queries for specific ranges. An index (idx) file must exist

Throws:

IOException

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(String featurePath,
 FeatureCodec<T,SOURCE> codec,
 boolean requireIndex,
 Function<SeekableByteChannel,SeekableByteChannel> wrapper,
 Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
                            throws IOException

Throws:

IOException

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(String featureFile,
 String indexFile,
 FeatureCodec<T,SOURCE> codec,
 boolean requireIndex)
                            throws IOException

Parameters:

featureFile - - path to the feature file, can be a local file path, http url, or ftp url

indexFile - - path to the index file

codec - - codec to decode the features

requireIndex - - true if the reader will be queries for specific ranges. An index (idx) file must exist

Throws:

IOException

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(String featureFile,
 String indexFile,
 FeatureCodec<T,SOURCE> codec,
 boolean requireIndex,
 Function<SeekableByteChannel,SeekableByteChannel> wrapper,
 Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
                            throws IOException

Parameters:

featureFile - - path to the feature file, can be a local file path, http url, or ftp url, or any other uri supported by a Path plugin

indexFile - - path to the index file

codec - - codec to decode the features

requireIndex - - true if the reader will be queries for specific ranges. An index (idx) file must exist

Throws:

IOException

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(String featureFile,
 FeatureCodec<T,SOURCE> codec,
 Index index)
                            throws IOException

Parameters:

featureFile - - path to the feature file, can be a local file path, http url, or ftp url

codec - - codec to decode the features

index - - a tribble Index object

Throws:

IOException

Method Details

close

public void close()
           throws IOException

Description copied from interface: FeatureReader

Closes the reader

Throws:

IOException

getSequenceNames

public List<String> getSequenceNames()

Return the sequence (chromosome/contig) names in this file, if known.

Returns:

list of strings of the contig names

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

isQueryable

public boolean isQueryable()

Specified by:

isQueryable in interface FeatureReader<T extends Feature>

Overrides:

isQueryable in class AbstractFeatureReader<T extends Feature,SOURCE>

Returns:

true if the reader has an index, which means that it can be queried.

query

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

Return an iterator to iterate over features overlapping the specified interval

Note that TribbleIndexedFeatureReader only supports issuing and manipulating a single query for each reader. That is, the behavior of the following code is undefined:

reader = new TribbleIndexedFeatureReader() Iterator it1 = reader.query("x", 10, 20) Iterator it2 = reader.query("x", 1000, 1010)

As a consequence of this, the TribbleIndexedFeatureReader are also not thread-safe.

Parameters:

chr - contig

start - start position

end - end position

Returns:

an iterator of records in this interval

Throws:

IOException

iterator

public CloseableTribbleIterator<T> iterator()
                                     throws IOException

Description copied from interface: FeatureReader

Provides access to all the features in the reader

Returns:

Return an iterator to iterate over the entire file

Throws:

IOException