org.broadinstitute.hellbender.engine

Interface ReadsDataSource

All Superinterfaces:

java.lang.AutoCloseable, GATKDataSource<GATKRead>, java.lang.Iterable<GATKRead>

All Known Implementing Classes:

ReadsPathDataSource

public interface ReadsDataSource
extends GATKDataSource<GATKRead>, java.lang.AutoCloseable

An interface for managing traversals over sources of reads. Two basic operations are available: -Iteration over all reads, optionally restricted to reads that overlap a set of intervals -Targeted queries by one interval at a time

Method Summary

Modifier and Type	Method and Description
void	close() Shut down this data source permanently, closing all iterations and readers.
htsjdk.samtools.SAMFileHeader	getHeader() Returns the SAM header for this data source.
default htsjdk.samtools.SAMSequenceDictionary	getSequenceDictionary() Get the sequence dictionary for this ReadsDataSource
boolean	isQueryableByInterval()
java.util.Iterator<GATKRead>	queryUnmapped()
default void	setTraversalBounds(java.util.List<SimpleInterval> intervals) Restricts a traversal of this data source via Iterable.iterator() to only return reads which overlap the given intervals.
void	setTraversalBounds(java.util.List<SimpleInterval> intervals, boolean traverseUnmapped) Restricts a traversal of this data source via Iterable.iterator() to only return reads that overlap the given intervals, and to unmapped reads if specified.
default void	setTraversalBounds(TraversalParameters traversalParameters) Restricts a traversal of this data source via Iterable.iterator() to only return reads that overlap the given intervals, and to unmapped reads if specified.
boolean	supportsSerialIteration()
boolean	traversalIsBounded()

Methods inherited from interface org.broadinstitute.hellbender.engine.GATKDataSource

query

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Method Detail

setTraversalBounds

void setTraversalBounds(java.util.List<SimpleInterval> intervals,
                        boolean traverseUnmapped)

Restricts a traversal of this data source via Iterable.iterator() to only return reads that overlap the given intervals, and to unmapped reads if specified. Calls to GATKDataSource.query(org.broadinstitute.hellbender.utils.SimpleInterval) are not affected by this method.

Parameters:

intervals - Our next full traversal will return reads overlapping these intervals

traverseUnmapped - Our next full traversal will return unmapped reads (this affects only unmapped reads that have no position -- unmapped reads that have the position of their mapped mates will be included if the interval overlapping that position is included).

setTraversalBounds

default void setTraversalBounds(java.util.List<SimpleInterval> intervals)

Restricts a traversal of this data source via Iterable.iterator() to only return reads which overlap the given intervals. Calls to GATKDataSource.query(org.broadinstitute.hellbender.utils.SimpleInterval) are not affected by setting these intervals.

Parameters:

intervals - Our next full traversal will return only reads overlapping these intervals

setTraversalBounds

default void setTraversalBounds(TraversalParameters traversalParameters)

Restricts a traversal of this data source via Iterable.iterator() to only return reads that overlap the given intervals, and to unmapped reads if specified. Calls to GATKDataSource.query(org.broadinstitute.hellbender.utils.SimpleInterval) are not affected by this method.

Parameters:

traversalParameters - set of traversal parameters to control which reads get returned by the next call to Iterable.iterator()

traversalIsBounded

boolean traversalIsBounded()

Returns:

true if traversals initiated via Iterable.iterator() will be restricted to reads that overlap intervals as configured via setTraversalBounds(java.util.List<org.broadinstitute.hellbender.utils.SimpleInterval>, boolean), otherwise false

isQueryableByInterval

boolean isQueryableByInterval()

Returns:

true if this datasource supports the query() operation otherwise false.

queryUnmapped

java.util.Iterator<GATKRead> queryUnmapped()

Returns:

An iterator over just the unmapped reads with no assigned position. This operation is not affected by prior calls to setTraversalBounds(java.util.List<org.broadinstitute.hellbender.utils.SimpleInterval>, boolean). The underlying file must be indexed.

getHeader

htsjdk.samtools.SAMFileHeader getHeader()

Returns the SAM header for this data source.

Returns:

SAM header for this data source

getSequenceDictionary

default htsjdk.samtools.SAMSequenceDictionary getSequenceDictionary()

Get the sequence dictionary for this ReadsDataSource

Returns:

SAMSequenceDictionary for the reads backing this datasource.

supportsSerialIteration

boolean supportsSerialIteration()

Returns:

true if this ReadsDataSource supports multiple iterations over the data

close

void close()

Shut down this data source permanently, closing all iterations and readers.

Specified by:

close in interface java.lang.AutoCloseable