org.broadinstitute.hellbender.tools.readersplitters

Class ReadGroupSplitter<T>

java.lang.Object

org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter<T>

org.broadinstitute.hellbender.tools.readersplitters.ReadGroupSplitter<T>

Type Parameters:

T - The type of the value from the read group.

Direct Known Subclasses:

LibraryNameSplitter, ReadGroupIdSplitter, SampleNameSplitter

public abstract class ReadGroupSplitter<T>
extends ReaderSplitter<T>

Splits a reader based on a value from a read group.

Constructor Summary

Constructors

Constructor and Description
ReadGroupSplitter()

Method Summary

Modifier and Type	Method and Description
T	getSplitBy(GATKRead record, htsjdk.samtools.SAMFileHeader header) Returns the value from this record for this splitter.
protected abstract java.util.function.Function<htsjdk.samtools.SAMReadGroupRecord,T>	getSplitByFunction()
java.util.List<T>	getSplitsBy(htsjdk.samtools.SAMFileHeader header) Returns the values from the header that will be used to split the reader.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadGroupSplitter

public ReadGroupSplitter()

Method Detail

getSplitBy

public T getSplitBy(GATKRead record,
                    htsjdk.samtools.SAMFileHeader header)

Description copied from class: ReaderSplitter

Returns the value from this record for this splitter.

Specified by:

getSplitBy in class ReaderSplitter<T>

Parameters:

record - The record.

header - Header for the record

Returns:

The value from the record for this splitter.

getSplitsBy

public java.util.List<T> getSplitsBy(htsjdk.samtools.SAMFileHeader header)

Description copied from class: ReaderSplitter

Returns the values from the header that will be used to split the reader.

Specified by:

getSplitsBy in class ReaderSplitter<T>

Parameters:

header - The header of the reader.

Returns:

The list of possibly values from the header for this splitter.

getSplitByFunction

protected abstract java.util.function.Function<htsjdk.samtools.SAMReadGroupRecord,T> getSplitByFunction()

Returns:

A function that selects a value from a read group record.