public class GenomicsDBFeatureReader<T extends htsjdk.tribble.Feature,SOURCE> extends Object implements htsjdk.tribble.FeatureReader<T>
FeatureReader
Currently, the reader only return VariantContext| Modifier and Type | Class and Description |
|---|---|
(package private) class |
GenomicsDBFeatureReader.GenomicsDBFeatureIterator
Iterator over
VariantContext objects. |
| 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 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
|
| 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 |
private String mLoaderJSONFile
private String mQueryJSONFile
protected htsjdk.tribble.FeatureCodecHeader mFCHeader
private htsjdk.variant.vcf.VCFHeader mVCFHeader
public GenomicsDBFeatureReader(String loaderJSONFile, String tiledbWorkspace, String arrayName, String referenceGenome, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) throws IOException
loaderJSONFile - GenomicsDB loader JSON configuration filetiledbWorkspace - TileDB workspace patharrayName - TileDB array namereferenceGenome - Path to reference genome (fasta file)codec - FeatureCodec, currently only BCF2Codec is testedIOException - when data cannot be read from the streampublic GenomicsDBFeatureReader(String loaderJSONFile, String tiledbWorkspace, String arrayName, String referenceGenome, String templateVCFHeaderFilename, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) throws IOException
loaderJSONFile - GenomicsDB loader JSON configuration filetiledbWorkspace - TileDB workspace patharrayName - TileDB array namereferenceGenome - Path to reference genome (fasta file)templateVCFHeaderFilename - Template VCF header to be used for
the combined gVCF recordscodec - FeatureCodec, currently only
BCF2Codec is testedIOException - when data cannot be read from the streampublic GenomicsDBFeatureReader(String loaderJSONFile, String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) throws IOException
loaderJSONFile - GenomicsDB loader JSON configuration filequeryJSONFile - GenomicsDB query JSON configuration filecodec - FeatureCodec, currently only BCF2Codec is testedIOException - when data cannot be read from the streampublic GenomicsDBFeatureReader(String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) throws IOException
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 JSONcodec - FeatureCodec, currently only BCF2Codec is testedIOException - when data cannot be read from the streampublic void initialize(String loaderJSONFile, String queryJSONFile, htsjdk.tribble.FeatureCodec<T,SOURCE> codec) throws IOException
loaderJSONFile - GenomicsDB loader JSON configuration filequeryJSONFile - GenomicsDB query JSON configuration filecodec - FeatureCodec, currently only BCF2Codec is testedIOException - when data cannot be read from the streampublic Object getHeader()
getHeader in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>public List<String> getSequenceNames()
getSequenceNames in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>public void close()
throws IOException
close in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>close in interface Closeableclose in interface AutoCloseableIOExceptionpublic htsjdk.tribble.CloseableTribbleIterator<T> iterator() throws IOException
VariantContext
objects for the specified TileDB array and query configurationiterator in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>VariantContext objectsIOExceptionpublic htsjdk.tribble.CloseableTribbleIterator<T> query(String chr, int start, int end) throws IOException
VariantContext
objects for the specified TileDB array and queried positionquery in interface htsjdk.tribble.FeatureReader<T extends htsjdk.tribble.Feature>chr - contig namestart - start position (1-based)end - end position, inclusive (1-based)VariantContext objectsIOExceptionCopyright © 2017. All rights reserved.