org.broadinstitute.hellbender.engine

Class AssemblyRegionIterator

java.lang.Object

org.broadinstitute.hellbender.engine.AssemblyRegionIterator

All Implemented Interfaces:

java.util.Iterator<AssemblyRegion>

public class AssemblyRegionIterator
extends java.lang.Object
implements java.util.Iterator<AssemblyRegion>

Given a MultiIntervalShard of GATKRead, iterates over each AssemblyRegion within that shard, using the provided AssemblyRegionEvaluator to determine the boundaries between assembly regions. Loads the reads from the shard as lazily as possible to minimize memory usage. This iterator represents the core of the AssemblyRegionWalker traversal. NOTE: the provided shard must have appropriate read filters set on it for this traversal type (ie., unmapped and malformed reads must be filtered out).

Constructor Summary

Constructors

Constructor and Description
AssemblyRegionIterator(MultiIntervalShard<GATKRead> readShard, htsjdk.samtools.SAMFileHeader readHeader, ReferenceDataSource reference, FeatureManager features, AssemblyRegionEvaluator evaluator, AssemblyRegionArgumentCollection assemblyRegionArgs) Constructs an AssemblyRegionIterator over a provided read shard

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
AssemblyRegion	next()
void	remove()

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

Constructor Detail

AssemblyRegionIterator

public AssemblyRegionIterator(MultiIntervalShard<GATKRead> readShard,
                              htsjdk.samtools.SAMFileHeader readHeader,
                              ReferenceDataSource reference,
                              FeatureManager features,
                              AssemblyRegionEvaluator evaluator,
                              AssemblyRegionArgumentCollection assemblyRegionArgs)

Constructs an AssemblyRegionIterator over a provided read shard

Parameters:

readShard - MultiIntervalShard containing the reads that will go into the assembly regions. Must have a MAPPED filter set on it.

readHeader - header for the reads

reference - source of reference bases (may be null)

features - source of arbitrary features (may be null)

evaluator - evaluator used to determine whether a locus is active

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<AssemblyRegion>

next

public AssemblyRegion next()

Specified by:

next in interface java.util.Iterator<AssemblyRegion>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<AssemblyRegion>