com.intel.genomicsdb

Class GenomicsDBFeatureReader.GenomicsDBFeatureIterator

java.lang.Object

com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<T>, htsjdk.tribble.CloseableTribbleIterator<T>, Closeable, AutoCloseable, Iterable<T>, Iterator<T>

Enclosing class:

GenomicsDBFeatureReader<T extends htsjdk.tribble.Feature,SOURCE>

class GenomicsDBFeatureReader.GenomicsDBFeatureIterator
extends Object
implements htsjdk.tribble.CloseableTribbleIterator<T>

Iterator over VariantContext objects. Uses GenomicsDBQueryStream to obtain combined gVCF records (as BCF2) from TileDB/GenomicsDB

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	mClosedBefore
private htsjdk.tribble.FeatureCodec<T,SOURCE>	mCodec
private SOURCE	mSource
private GenomicsDBQueryStream	mStream
private GenomicsDBTimer	mTimer

Constructor Summary

Constructors

Constructor and Description
GenomicsDBFeatureIterator(String loaderJSONFile, String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) Constructor
GenomicsDBFeatureIterator(String loaderJSONFile, String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec, String chr, int start, int end) Constructor

Method Summary

Modifier and Type	Method and Description
void	close()
boolean	hasNext()
GenomicsDBFeatureReader.GenomicsDBFeatureIterator	iterator()
T	next()
void	remove()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

mCodec

private htsjdk.tribble.FeatureCodec<T extends htsjdk.tribble.Feature,SOURCE> mCodec

mStream

private GenomicsDBQueryStream mStream

mSource

private SOURCE mSource

mTimer

private GenomicsDBTimer mTimer

mClosedBefore

private boolean mClosedBefore

Constructor Detail

GenomicsDBFeatureIterator

public GenomicsDBFeatureIterator(String loaderJSONFile,
                                 String queryJSONFile,
                                 htsjdk.tribble.FeatureCodec<T,SOURCE> codec)
                          throws IOException

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

queryJSONFile - GenomicsDB query JSON configuration file

codec - FeatureCodec, currently only BCF2Codec is tested

Throws:

IOException - when data cannot be read from the stream

GenomicsDBFeatureIterator

public GenomicsDBFeatureIterator(String loaderJSONFile,
                                 String queryJSONFile,
                                 htsjdk.tribble.FeatureCodec<T,SOURCE> codec,
                                 String chr,
                                 int start,
                                 int end)
                          throws IOException

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

queryJSONFile - GenomicsDB query JSON configuration file

codec - FeatureCodec, currently only BCF2Codec is tested

chr - contig name

start - start position (1-based)

end - end position, inclusive (1-based)

Throws:

IOException - when data cannot be read from the stream

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<T extends htsjdk.tribble.Feature>

next

public T next()

Specified by:

next in interface Iterator<T extends htsjdk.tribble.Feature>

close

public void close()

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<T extends htsjdk.tribble.Feature>

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

iterator

public GenomicsDBFeatureReader.GenomicsDBFeatureIterator iterator()

Specified by:

iterator in interface Iterable<T extends htsjdk.tribble.Feature>

remove

public void remove()

Specified by:

remove in interface Iterator<T extends htsjdk.tribble.Feature>