FeatureReader (htsjdk 2.14.3 API)

Type Parameters:

T - a feature type

All Superinterfaces:

AutoCloseable, Closeable

All Known Implementing Classes:

AbstractFeatureReader, TabixFeatureReader, TribbleIndexedFeatureReader
```
public interface FeatureReader<T extends Feature>
extends Closeable
```
the basic interface that feature sources need to match

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`void`	`close()`	Closes the reader
`Object`	`getHeader()`	Provide access to the header of the reader
`List<String>`	`getSequenceNames()`	Provides the list of sequenceNames if known.
`default boolean`	`isQueryable()`
`CloseableTribbleIterator<T>`	`iterator()`	Provides access to all the features in the reader
`default CloseableTribbleIterator<T>`	`query(Locatable locus)`	Query the reader for a particular interval corresponding to a contig and a 1-based closed
`CloseableTribbleIterator<T>`	`query(String chr, int start, int end)`	Query the reader for a particular interval corresponding to a contig and a 1-based closed

- Method Detail
  - query
```
CloseableTribbleIterator<T> query(String chr,
                                  int start,
                                  int end)
                           throws IOException
```
    Query the reader for a particular interval corresponding to a contig and a 1-based closed
    
    Parameters:
    
    chr - the contig to be queried
    
    start - the start of the interval (1-based) to be queried
    
    end - the last base in the interval to be queried
    
    Returns:
    
    an iterator containing the features that at in the interval.
    
    Throws:
    
    IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.
  - query
```
default CloseableTribbleIterator<T> query(Locatable locus)
                                   throws IOException
```
    Query the reader for a particular interval corresponding to a contig and a 1-based closed
    
    Parameters:
    
    locus - The locus to be queried
    
    Returns:
    
    an iterator containing the features that at in the interval.
    
    Throws:
    
    IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.
  - iterator
```
CloseableTribbleIterator<T> iterator()
                              throws IOException
```
    Provides access to all the features in the reader
    
    Returns:
    
    an iterator to all the features in the reader
    
    Throws:
    
    IOException - If there's a problem reading.
  - close
```
void close()
    throws IOException
```
    Closes the reader
    
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Throws:
    
    IOException
  - getSequenceNames
```
List<String> getSequenceNames()
```
    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.
  - getHeader
```
Object getHeader()
```
    Provide access to the header of the reader
    
    Returns:
    
    the header of the reader. May be null.
  - isQueryable
```
default boolean isQueryable()
```
    Returns:
    
    true if the reader has an index, which means that it can be queried. Must be implemented to return true if the implementation supports query(Locatable)

Interface FeatureReader<T extends Feature>

Method Summary

Method Detail

query

query

iterator

close

getSequenceNames

getHeader

isQueryable