com.intel.genomicsdb

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

java.lang.Object

com.intel.genomicsdb.GenomicsDBFeatureReader<T,SOURCE>

All Implemented Interfaces:

htsjdk.tribble.FeatureReader<T>, Closeable, AutoCloseable

public class GenomicsDBFeatureReader<T extends htsjdk.tribble.Feature,SOURCE>
extends Object
implements htsjdk.tribble.FeatureReader<T>

A reader for GenomicsDB that implements FeatureReader Currently, the reader only return VariantContext

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	GenomicsDBFeatureReader.GenomicsDBFeatureIterator Iterator over VariantContext objects.

Field Summary

Fields

Modifier and Type	Field and Description
private htsjdk.tribble.FeatureCodec<T,SOURCE>	mCodec
protected htsjdk.tribble.FeatureCodecHeader	mFCHeader
private String	mLoaderJSONFile
private String	mQueryJSONFile
private ArrayList<String>	mSequenceNames
private htsjdk.variant.vcf.VCFHeader	mVCFHeader

Constructor Summary

Constructors

Constructor and Description
GenomicsDBFeatureReader(String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) Constructor
GenomicsDBFeatureReader(String loaderJSONFile, String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) Constructor
GenomicsDBFeatureReader(String loaderJSONFile, String tiledbWorkspace, String arrayName, String referenceGenome, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) Constructor
GenomicsDBFeatureReader(String loaderJSONFile, String tiledbWorkspace, String arrayName, String referenceGenome, String templateVCFHeaderFilename, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) Constructor

Method Summary

Modifier and Type	Method and Description
void	close()
Object	getHeader() Return the VCF header of the combined gVCF stream
List<String>	getSequenceNames() Return the list of contigs in the combined VCF header
void	initialize(String loaderJSONFile, String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) Initialization function that's used by all constructors
htsjdk.tribble.CloseableTribbleIterator<T>	iterator() Return an iterator over VariantContext objects for the specified TileDB array and query configuration
htsjdk.tribble.CloseableTribbleIterator<T>	query(String chr, int start, int end) Return an iterator over VariantContext objects for the specified TileDB array and queried position

Methods inherited from class java.lang.Object

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

Field Detail

mLoaderJSONFile

private String mLoaderJSONFile

mQueryJSONFile

private String mQueryJSONFile

mCodec

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

mFCHeader

protected htsjdk.tribble.FeatureCodecHeader mFCHeader

mVCFHeader

private htsjdk.variant.vcf.VCFHeader mVCFHeader

mSequenceNames

private ArrayList<String> mSequenceNames

Constructor Detail

GenomicsDBFeatureReader

public GenomicsDBFeatureReader(String loaderJSONFile,
                               String tiledbWorkspace,
                               String arrayName,
                               String referenceGenome,
                               htsjdk.tribble.FeatureCodec<T,SOURCE> codec)
                        throws IOException

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

tiledbWorkspace - TileDB workspace path

arrayName - TileDB array name

referenceGenome - Path to reference genome (fasta file)

codec - FeatureCodec, currently only BCF2Codec is tested

Throws:

IOException - when data cannot be read from the stream

GenomicsDBFeatureReader

public GenomicsDBFeatureReader(String loaderJSONFile,
                               String tiledbWorkspace,
                               String arrayName,
                               String referenceGenome,
                               String templateVCFHeaderFilename,
                               htsjdk.tribble.FeatureCodec<T,SOURCE> codec)
                        throws IOException

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

tiledbWorkspace - TileDB workspace path

arrayName - TileDB array name

referenceGenome - Path to reference genome (fasta file)

templateVCFHeaderFilename - Template VCF header to be used for the combined gVCF records

codec - FeatureCodec, currently only BCF2Codec is tested

Throws:

IOException - when data cannot be read from the stream

GenomicsDBFeatureReader

public GenomicsDBFeatureReader(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

GenomicsDBFeatureReader

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

Constructor

Parameters:

queryJSONFile - GenomicsDB query JSON configuration file. Since the constructor has no loader JSON as argument, you must specify the vid and callset mapping in the query JSON

codec - FeatureCodec, currently only BCF2Codec is tested

Throws:

IOException - when data cannot be read from the stream

Method Detail

initialize

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

Initialization function that's used by all constructors

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

getHeader

public Object getHeader()

Return the VCF header of the combined gVCF stream

Specified by:

getHeader in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

Returns:

the VCF header of the combined gVCF stream

getSequenceNames

public List<String> getSequenceNames()

Return the list of contigs in the combined VCF header

Specified by:

getSequenceNames in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

Returns:

list of strings of the contig names

close

public void close()
           throws IOException

Specified by:

close in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Throws:

IOException

iterator

public htsjdk.tribble.CloseableTribbleIterator<T> iterator()
                                                    throws IOException

Return an iterator over VariantContext objects for the specified TileDB array and query configuration

Specified by:

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

Returns:

iterator over VariantContext objects

Throws:

IOException

query

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

Return an iterator over VariantContext objects for the specified TileDB array and queried position

Specified by:

query in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>

Parameters:

chr - contig name

start - start position (1-based)

end - end position, inclusive (1-based)

Returns:

iterator over VariantContext objects

Throws:

IOException