com.intel.genomicsdb

Class MultiChromosomeIterator<SOURCE>

java.lang.Object

com.intel.genomicsdb.MultiChromosomeIterator<SOURCE>

Type Parameters:

SOURCE - LineIterator for VCFs, PositionalBufferedStream for BCFs

All Implemented Interfaces:

Iterator<htsjdk.variant.variantcontext.VariantContext>

class MultiChromosomeIterator<SOURCE>
extends Object
implements Iterator<htsjdk.variant.variantcontext.VariantContext>

Given an AbstractFeatureReader over VariantContext objects and a list of ChromosomeInterval objects, this class is an Iterator over VariantContext for all the chromosome intervals in the list

Field Summary

Fields

Modifier and Type	Field and Description
private ArrayList<ChromosomeInterval>	mChromosomeIntervals
private int	mIdxInIntervalList
private htsjdk.tribble.CloseableTribbleIterator<htsjdk.variant.variantcontext.VariantContext>	mIterator
private htsjdk.tribble.AbstractFeatureReader<htsjdk.variant.variantcontext.VariantContext,SOURCE>	mReader

Constructor Summary

Constructors

Constructor and Description
MultiChromosomeIterator(htsjdk.tribble.AbstractFeatureReader<htsjdk.variant.variantcontext.VariantContext,SOURCE> reader, List<ChromosomeInterval> chromosomeIntervals) Constructor

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
htsjdk.variant.variantcontext.VariantContext	next()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Field Detail

mChromosomeIntervals

private ArrayList<ChromosomeInterval> mChromosomeIntervals

mReader

private htsjdk.tribble.AbstractFeatureReader<htsjdk.variant.variantcontext.VariantContext,SOURCE> mReader

mIdxInIntervalList

private int mIdxInIntervalList

mIterator

private htsjdk.tribble.CloseableTribbleIterator<htsjdk.variant.variantcontext.VariantContext> mIterator

Constructor Detail

MultiChromosomeIterator

MultiChromosomeIterator(htsjdk.tribble.AbstractFeatureReader<htsjdk.variant.variantcontext.VariantContext,SOURCE> reader,
                        List<ChromosomeInterval> chromosomeIntervals)
                 throws IOException

Constructor

Parameters:

reader - AbstractFeatureReader over VariantContext objects - SOURCE can vary - BCF v/s VCF for example

chromosomeIntervals - chromosome intervals over which to iterate

Throws:

IOException - when the reader's query method throws an IOException

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<htsjdk.variant.variantcontext.VariantContext>

next

public htsjdk.variant.variantcontext.VariantContext next()
                                                  throws NoSuchElementException

Specified by:

next in interface Iterator<htsjdk.variant.variantcontext.VariantContext>

Throws:

NoSuchElementException