org.broadinstitute.hellbender.utils.read.markduplicates

Class LibraryIdGenerator

java.lang.Object

org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator

public final class LibraryIdGenerator
extends java.lang.Object

A class to generate library Ids and keep duplication metrics by library IDs.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	UNKNOWN_LIBRARY

Constructor Summary

Constructors

Constructor and Description
LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header)

Method Summary

Modifier and Type	Method and Description
void	addMetricsByLibrary(java.lang.String library, GATKDuplicationMetrics metrics)
short	getLibraryId(htsjdk.samtools.SAMRecord rec) Get the library ID for the given SAM record.
java.util.Map<java.lang.String,java.lang.Short>	getLibraryIdsMap()
static java.lang.String	getLibraryName(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec) Gets the library name from the header for the record.
static java.lang.String	getLibraryName(htsjdk.samtools.SAMFileHeader header, java.lang.String readGroupId) Gets the library name from the header for the read group id.
GATKDuplicationMetrics	getMetricsByLibrary(java.lang.String library)
java.util.Map<java.lang.String,GATKDuplicationMetrics>	getMetricsByLibraryMap()
long	getNumberOfOpticalDuplicateClusters()
htsjdk.samtools.util.Histogram<java.lang.Short>	getOpticalDuplicatesByLibraryIdMap()
static java.lang.String	getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup)

Methods inherited from class java.lang.Object

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

Field Detail

UNKNOWN_LIBRARY

public static final java.lang.String UNKNOWN_LIBRARY

See Also:

Constant Field Values

Constructor Detail

LibraryIdGenerator

public LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header)

Method Detail

getLibraryIdsMap

public java.util.Map<java.lang.String,java.lang.Short> getLibraryIdsMap()

getMetricsByLibraryMap

public java.util.Map<java.lang.String,GATKDuplicationMetrics> getMetricsByLibraryMap()

getOpticalDuplicatesByLibraryIdMap

public htsjdk.samtools.util.Histogram<java.lang.Short> getOpticalDuplicatesByLibraryIdMap()

getReadGroupLibraryName

public static java.lang.String getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup)

getLibraryName

public static java.lang.String getLibraryName(htsjdk.samtools.SAMFileHeader header,
                                              htsjdk.samtools.SAMRecord rec)

Gets the library name from the header for the record. If the RG tag is not present on the record, or the library isn't denoted on the read group, a constant string is returned.

getLibraryName

public static java.lang.String getLibraryName(htsjdk.samtools.SAMFileHeader header,
                                              java.lang.String readGroupId)

Gets the library name from the header for the read group id. If the read group id is null or the library isn't denoted on the read group, a constant string is returned.

getLibraryId

public short getLibraryId(htsjdk.samtools.SAMRecord rec)

Get the library ID for the given SAM record.

getMetricsByLibrary

public GATKDuplicationMetrics getMetricsByLibrary(java.lang.String library)

addMetricsByLibrary

public void addMetricsByLibrary(java.lang.String library,
                                GATKDuplicationMetrics metrics)

getNumberOfOpticalDuplicateClusters

public long getNumberOfOpticalDuplicateClusters()