org.broadinstitute.hellbender.engine

Class MultiIntervalLocalReadShard

java.lang.Object

org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard

All Implemented Interfaces:

java.lang.Iterable<GATKRead>, MultiIntervalShard<GATKRead>

public final class MultiIntervalLocalReadShard
extends java.lang.Object
implements MultiIntervalShard<GATKRead>

A class to represent shards of read data spanning multiple intervals. The reads are lazily loaded by default (when calling iterator()). The reads returned will overlap the intervals, including any padding requested. Shards may be configured to apply custom filters, transformers and downsamplers to the stream of reads returned by iterator(). IMPORTANT: For efficiency, all intervals within each shard are queried simultaneously. This avoids the problem of decompressing the same file regions multiple times for intervals that are close together, and is critical for performance!

Constructor Summary

Constructors

Constructor and Description
MultiIntervalLocalReadShard(java.util.List<SimpleInterval> intervals, int intervalPadding, ReadsDataSource readsSource) Create a new MultiIntervalLocalReadShard spanning the given intervals, with each interval expanded on both sides by the specified number of padding bases.
MultiIntervalLocalReadShard(java.util.List<SimpleInterval> intervals, ReadsDataSource readsSource) Create a new MultiIntervalLocalReadShard spanning the given intervals, with no padding around intervals.

Method Summary

Modifier and Type	Method and Description
java.util.List<SimpleInterval>	getIntervals()
java.util.List<SimpleInterval>	getPaddedIntervals()
java.util.Iterator<GATKRead>	iterator()
void	setDownsampler(ReadsDownsampler downsampler) Reads in this shard will be downsampled using this downsampler before being returned.
void	setPostReadFilterTransformer(ReadTransformer transformer) Reads in this shard will be transformed after filtering and before downsampling
void	setPreReadFilterTransformer(ReadTransformer transformer) Reads in this shard will be transformed before filtering
void	setReadFilter(ReadFilter filter) Reads in this shard will be filtered using this filter before being returned.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

MultiIntervalLocalReadShard

public MultiIntervalLocalReadShard(java.util.List<SimpleInterval> intervals,
                                   int intervalPadding,
                                   ReadsDataSource readsSource)

Create a new MultiIntervalLocalReadShard spanning the given intervals, with each interval expanded on both sides by the specified number of padding bases.

Parameters:

intervals - The intervals that this shard spans

intervalPadding - Number of bases to pad each of the shard's intervals (on both sides)

readsSource - Source of reads

MultiIntervalLocalReadShard

public MultiIntervalLocalReadShard(java.util.List<SimpleInterval> intervals,
                                   ReadsDataSource readsSource)

Create a new MultiIntervalLocalReadShard spanning the given intervals, with no padding around intervals.

Parameters:

intervals - The intervals that this shard spans

readsSource - Source of reads

Method Detail

getIntervals

public java.util.List<SimpleInterval> getIntervals()

Specified by:

getIntervals in interface MultiIntervalShard<GATKRead>

Returns:

A List of this shard's intervals

getPaddedIntervals

public java.util.List<SimpleInterval> getPaddedIntervals()

Specified by:

getPaddedIntervals in interface MultiIntervalShard<GATKRead>

Returns:

A List of this shard's intervals, with padding added to each interval on both sides

setPreReadFilterTransformer

public void setPreReadFilterTransformer(ReadTransformer transformer)

Reads in this shard will be transformed before filtering

Parameters:

transformer - read transformer to apply before read filtering

setReadFilter

public void setReadFilter(ReadFilter filter)

Reads in this shard will be filtered using this filter before being returned. Read filtering will be performed before any requested downsampling.

Parameters:

filter - filter to use (may be null, which signifies that no filtering is to be performed)

setDownsampler

public void setDownsampler(ReadsDownsampler downsampler)

Reads in this shard will be downsampled using this downsampler before being returned. Downsampling will be performed after any requested read filtering.

Parameters:

downsampler - downsampler to use (may be null, which signifies that no downsampling is to be performed)

setPostReadFilterTransformer

public void setPostReadFilterTransformer(ReadTransformer transformer)

Reads in this shard will be transformed after filtering and before downsampling

Parameters:

transformer - read transformer to apply after read filtering and before downsampling

iterator

public java.util.Iterator<GATKRead> iterator()

Specified by:

iterator in interface java.lang.Iterable<GATKRead>

Returns:

an iterator over reads in this shard, as filtered using the configured read filter and downsampled using the configured downsampler; reads are lazily loaded rather than pre-loaded Note that any read filtering is always performed before any downsampling.