com.intel.genomicsdb

Class GenomicsDBImporterStreamWrapper

java.lang.Object

com.intel.genomicsdb.GenomicsDBImporterStreamWrapper

class GenomicsDBImporterStreamWrapper
extends Object

Utility class wrapping a stream and a VariantContextWriter for a given stream Each GenomicsDB import stream consists of a buffer stream and a writer object If the caller provides an iterator, then mCurrentVC points to the VariantContext object to be written, if any.

Field Summary

Fields

Modifier and Type	Field and Description
private htsjdk.variant.variantcontext.VariantContext	mCurrentVC
private Iterator<htsjdk.variant.variantcontext.VariantContext>	mIterator
(package private) SilentByteBufferStream	mStream
(package private) htsjdk.variant.variantcontext.writer.VariantContextWriter	mVCWriter

Constructor Summary

Constructors

Constructor and Description
GenomicsDBImporterStreamWrapper(htsjdk.variant.vcf.VCFHeader vcfHeader, long bufferCapacity, htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType, Iterator<htsjdk.variant.variantcontext.VariantContext> vcIterator) Constructor

Method Summary

Modifier and Type	Method and Description
(package private) htsjdk.variant.variantcontext.VariantContext	getCurrentVC() Returns mCurrentVC - could be null if mIterator is null or !mIterator.hasNext()
(package private) boolean	hasIterator() Returns true if a non-null Iterator over VariantContext objects was provided for this stream
htsjdk.variant.variantcontext.VariantContext	next() Returns the next VariantContext object iff the Iterator over VariantContext objects is non-null and has a next() object, else returns null.

Methods inherited from class java.lang.Object

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

Field Detail

mVCWriter

htsjdk.variant.variantcontext.writer.VariantContextWriter mVCWriter

mStream

SilentByteBufferStream mStream

mIterator

private Iterator<htsjdk.variant.variantcontext.VariantContext> mIterator

mCurrentVC

private htsjdk.variant.variantcontext.VariantContext mCurrentVC

Constructor Detail

GenomicsDBImporterStreamWrapper

public GenomicsDBImporterStreamWrapper(htsjdk.variant.vcf.VCFHeader vcfHeader,
                                       long bufferCapacity,
                                       htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType,
                                       Iterator<htsjdk.variant.variantcontext.VariantContext> vcIterator)
                                throws GenomicsDBException

Constructor

Parameters:

vcfHeader - VCF header for the stream

bufferCapacity - Capacity of the stream buffer in bytes

streamType - BCF_STREAM or VCF_STREAM

vcIterator - iterator over VariantContext objects, can be null if the caller is managing the buffer explicitly

Throws:

GenomicsDBException

Method Detail

hasIterator

boolean hasIterator()

Returns true if a non-null Iterator over VariantContext objects was provided for this stream

Returns:

True if iterator was provided, False otherwise

next

public htsjdk.variant.variantcontext.VariantContext next()

Returns the next VariantContext object iff the Iterator over VariantContext objects is non-null and has a next() object, else returns null. Stores the result in mCurrentVC

Returns:

the next VariantContext object or null

getCurrentVC

htsjdk.variant.variantcontext.VariantContext getCurrentVC()

Returns mCurrentVC - could be null if mIterator is null or !mIterator.hasNext()

Returns:

VariantContext object to be written