com.intel.genomicsdb

Class GenomicsDBQueryStream

java.lang.Object

java.io.InputStream

com.intel.genomicsdb.GenomicsDBQueryStream

All Implemented Interfaces:

Closeable, AutoCloseable

public class GenomicsDBQueryStream
extends InputStream

Provides a java.io.InputStream interface for the GenomicsDB combine gVCF operation. It can be used as to construct a PositionalBufferedStream object.The PositionalBufferedStream object can then be used by FeatureCodecs such as BCF2Codec to construct VariantContext objects

Field Summary

Fields

Modifier and Type	Field and Description
private long	mGenomicsDBReadStateHandle
private String	mLoaderJSONFile
private String	mQueryJSONFile

Constructor Summary

Constructors

Constructor and Description
GenomicsDBQueryStream(String loaderJSONFile, String queryJSONFile) Constructor
GenomicsDBQueryStream(String loaderJSONFile, String queryJSONFile, String chr, int start, int end) Constructor
GenomicsDBQueryStream(String loaderJSONFile, String queryJSONFile, String chr, int start, int end, int rank) Constructor
GenomicsDBQueryStream(String loaderJSONFile, String queryJSONFile, String chr, int start, int end, int rank, long bufferCapacity, long segmentSize) Constructor

Method Summary

Modifier and Type	Method and Description
int	available()
void	close()
private long	jniGenomicsDBClose(long handle)
private long	jniGenomicsDBGetNumBytesAvailable(long handle)
private long	jniGenomicsDBInit(String loaderJSONFile, String queryJSONFile, String chr, int start, int end, int rank, long bufferCapacity, long segmentSize)
private int	jniGenomicsDBRead(long handle, byte[] buffer, int off, int len)
private byte	jniGenomicsDBReadNextByte(long handle)
private long	jniGenomicsDBSkip(long handle, long n)
boolean	markSupported()
int	read()
int	read(byte[] buffer, int off, int len)
long	skip(long n)

Methods inherited from class java.io.InputStream

mark, read, reset

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

mGenomicsDBReadStateHandle

private long mGenomicsDBReadStateHandle

Constructor Detail

GenomicsDBQueryStream

public GenomicsDBQueryStream(String loaderJSONFile,
                             String queryJSONFile)

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

queryJSONFile - GenomicsDB query JSON configuration file

GenomicsDBQueryStream

public GenomicsDBQueryStream(String loaderJSONFile,
                             String queryJSONFile,
                             String chr,
                             int start,
                             int end)

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

queryJSONFile - GenomicsDB query JSON configuration file

chr - contig name

start - start position (1-based)

end - end position, inclusive (1-based)

GenomicsDBQueryStream

public GenomicsDBQueryStream(String loaderJSONFile,
                             String queryJSONFile,
                             String chr,
                             int start,
                             int end,
                             int rank)

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

queryJSONFile - GenomicsDB query JSON configuration file

chr - contig name

start - start position (1-based)

end - end position, inclusive (1-based)

rank - rank of this object if launched from within an MPI context (not used)

GenomicsDBQueryStream

public GenomicsDBQueryStream(String loaderJSONFile,
                             String queryJSONFile,
                             String chr,
                             int start,
                             int end,
                             int rank,
                             long bufferCapacity,
                             long segmentSize)

Constructor

Parameters:

loaderJSONFile - GenomicsDB loader JSON configuration file

queryJSONFile - GenomicsDB query JSON configuration file

chr - contig name

start - start position (1-based)

end - end position, inclusive (1-based)

rank - rank of this object if launched from within an MPI context (not used)

bufferCapacity - size of buffer in bytes to be used by the native layer to store combined BCF2 records

segmentSize - buffer to be used for querying TileDB

Method Detail

jniGenomicsDBInit

private long jniGenomicsDBInit(String loaderJSONFile,
                               String queryJSONFile,
                               String chr,
                               int start,
                               int end,
                               int rank,
                               long bufferCapacity,
                               long segmentSize)

jniGenomicsDBClose

private long jniGenomicsDBClose(long handle)

jniGenomicsDBGetNumBytesAvailable

private long jniGenomicsDBGetNumBytesAvailable(long handle)

jniGenomicsDBReadNextByte

private byte jniGenomicsDBReadNextByte(long handle)

jniGenomicsDBRead

private int jniGenomicsDBRead(long handle,
                              byte[] buffer,
                              int off,
                              int len)

jniGenomicsDBSkip

private long jniGenomicsDBSkip(long handle,
                               long n)

available

public int available()
              throws IOException

Overrides:

available in class InputStream

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class InputStream

Throws:

IOException

markSupported

public boolean markSupported()

Overrides:

markSupported in class InputStream

read

public int read()
         throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

public int read(byte[] buffer,
                int off,
                int len)
         throws IOException

Overrides:

read in class InputStream

Throws:

IOException

skip

public long skip(long n)
          throws IOException

Overrides:

skip in class InputStream

Throws:

IOException