public class TabixFeatureReader<T extends Feature,SOURCE> extends AbstractFeatureReader<T,SOURCE>
AbstractFeatureReader.ComponentMethodsBLOCK_COMPRESSED_EXTENSIONS, codec, header| Constructor and Description |
|---|
TabixFeatureReader(String featureFile,
AsciiFeatureCodec codec) |
TabixFeatureReader(String featureFile,
String indexFile,
AsciiFeatureCodec codec) |
| Modifier and Type | Method and Description |
|---|---|
void |
close() |
List<String> |
getSequenceNames() |
boolean |
hasIndex()
Whether the reader has an index or not
Default implementation returns false
|
CloseableTribbleIterator<T> |
iterator() |
CloseableTribbleIterator<T> |
query(String chr,
int start,
int end)
Return iterator over all features overlapping the given interval
|
getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, hasBlockCompressedExtension, setComponentMethodspublic TabixFeatureReader(String featureFile, AsciiFeatureCodec codec) throws IOException
featureFile - - path to a feature file. Can be a local file, http url, or ftp urlcodec - IOExceptionpublic TabixFeatureReader(String featureFile, String indexFile, AsciiFeatureCodec codec) throws IOException
featureFile - - path to a feature file. Can be a local file, http url, or ftp urlindexFile - - path to the index file.codec - IOExceptionpublic boolean hasIndex()
AbstractFeatureReaderhasIndex in class AbstractFeatureReader<T extends Feature,SOURCE>public CloseableTribbleIterator<T> query(String chr, int start, int end) throws IOException
chr - start - end - IOExceptionpublic CloseableTribbleIterator<T> iterator() throws IOException
IOExceptionpublic void close()
throws IOException
IOException