org.broadinstitute.hellbender.engine

Class ActivityProfileStateIterator

java.lang.Object

org.broadinstitute.hellbender.engine.ActivityProfileStateIterator

All Implemented Interfaces:

java.util.Iterator<ActivityProfileState>

public class ActivityProfileStateIterator
extends java.lang.Object
implements java.util.Iterator<ActivityProfileState>

Given a MultiIntervalShard of GATKRead, iterates over each locus within that shard, and calculates the ActivityProfileState there, using the provided AssemblyRegionEvaluator to determine if each site is active. Loads the reads from the shard as lazily as possible to minimize memory usage. 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
ActivityProfileStateIterator(MultiIntervalShard<GATKRead> readShard, htsjdk.samtools.SAMFileHeader readHeader, ReferenceDataSource reference, FeatureManager features, AssemblyRegionEvaluator evaluator) Constructs an AssemblyRegionIterator over a provided read shard

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
ActivityProfileState	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

ActivityProfileStateIterator

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

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<ActivityProfileState>

next

public ActivityProfileState next()

Specified by:

next in interface java.util.Iterator<ActivityProfileState>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<ActivityProfileState>