public class TribbleIndexedFeatureReader<T extends Feature,SOURCE> extends AbstractFeatureReader<T,SOURCE>
AbstractFeatureReader.ComponentMethods
BLOCK_COMPRESSED_EXTENSIONS, codec, header
Constructor and Description |
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TribbleIndexedFeatureReader(java.lang.String featurePath,
FeatureCodec<T,SOURCE> codec,
boolean requireIndex) |
TribbleIndexedFeatureReader(java.lang.String featurePath,
FeatureCodec<T,SOURCE> codec,
boolean requireIndex,
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) |
TribbleIndexedFeatureReader(java.lang.String featureFile,
FeatureCodec<T,SOURCE> codec,
Index index) |
TribbleIndexedFeatureReader(java.lang.String featureFile,
java.lang.String indexFile,
FeatureCodec<T,SOURCE> codec,
boolean requireIndex) |
TribbleIndexedFeatureReader(java.lang.String featureFile,
java.lang.String indexFile,
FeatureCodec<T,SOURCE> codec,
boolean requireIndex,
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) |
Modifier and Type | Method and Description |
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void |
close()
Closes the reader
|
java.util.List<java.lang.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(java.lang.String chr,
int start,
int end)
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.
|
getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, hasBlockCompressedExtension, isTabix, setComponentMethods
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
query
public TribbleIndexedFeatureReader(java.lang.String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex) throws java.io.IOException
featurePath
- - path to the feature file, can be a local file path, http url, or ftp urlcodec
- - codec to decode the featuresrequireIndex
- - true if the reader will be queries for specific ranges. An index (idx) file must existjava.io.IOException
public TribbleIndexedFeatureReader(java.lang.String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex, 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
java.io.IOException
public TribbleIndexedFeatureReader(java.lang.String featureFile, java.lang.String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex) throws java.io.IOException
featureFile
- - path to the feature file, can be a local file path, http url, or ftp urlindexFile
- - path to the index filecodec
- - codec to decode the featuresrequireIndex
- - true if the reader will be queries for specific ranges. An index (idx) file must existjava.io.IOException
public TribbleIndexedFeatureReader(java.lang.String featureFile, java.lang.String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex, 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
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
pluginindexFile
- - path to the index filecodec
- - codec to decode the featuresrequireIndex
- - true if the reader will be queries for specific ranges. An index (idx) file must existjava.io.IOException
public TribbleIndexedFeatureReader(java.lang.String featureFile, FeatureCodec<T,SOURCE> codec, Index index) throws java.io.IOException
featureFile
- - path to the feature file, can be a local file path, http url, or ftp urlcodec
- - codec to decode the featuresindex
- - a tribble Index objectjava.io.IOException
public void close() throws java.io.IOException
FeatureReader
java.io.IOException
public java.util.List<java.lang.String> getSequenceNames()
public boolean hasIndex()
AbstractFeatureReader
hasIndex
in class AbstractFeatureReader<T extends Feature,SOURCE>
public boolean isQueryable()
isQueryable
in interface FeatureReader<T extends Feature>
isQueryable
in class AbstractFeatureReader<T extends Feature,SOURCE>
public CloseableTribbleIterator<T> query(java.lang.String chr, int start, int end) throws java.io.IOException
chr
- contigstart
- start positionend
- end positionjava.io.IOException
public CloseableTribbleIterator<T> iterator() throws java.io.IOException
FeatureReader
java.io.IOException