htsjdk.samtools

Class SAMReadGroupRecord

java.lang.Object

htsjdk.samtools.AbstractSAMHeaderRecord

htsjdk.samtools.SAMReadGroupRecord

All Implemented Interfaces:

java.io.Serializable

public class SAMReadGroupRecord
extends AbstractSAMHeaderRecord

Header information about a read group.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SAMReadGroupRecord.PlatformValue

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DATE_RUN_PRODUCED_TAG
static java.lang.String	DESCRIPTION_TAG
static java.lang.String	FLOW_ORDER_TAG
static java.lang.String	KEY_SEQUENCE_TAG
static java.lang.String	LIBRARY_TAG
static java.lang.String	PLATFORM_MODEL_TAG
static java.lang.String	PLATFORM_TAG
static java.lang.String	PLATFORM_UNIT_TAG
static java.lang.String	PREDICTED_MEDIAN_INSERT_SIZE_TAG
static java.lang.String	PROGRAM_GROUP_TAG
static java.lang.String	READ_GROUP_ID_TAG
static java.lang.String	READ_GROUP_SAMPLE_TAG
static java.lang.String	SEQUENCING_CENTER_TAG
static java.util.Set<java.lang.String>	STANDARD_TAGS

Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMReadGroupRecord(java.lang.String id)
SAMReadGroupRecord(java.lang.String id, SAMReadGroupRecord srcProgramRecord)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
boolean	equivalent(SAMReadGroupRecord that)
java.lang.String	getDescription()
java.lang.String	getFlowOrder()
java.lang.String	getId() Returns the ID tag (or equivalent) for this header record.
java.lang.String	getKeySequence()
java.lang.String	getLibrary()
java.lang.String	getPlatform()
java.lang.String	getPlatformModel()
java.lang.String	getPlatformUnit()
java.lang.Integer	getPredictedMedianInsertSize()
java.lang.String	getProgramGroup()
java.lang.String	getReadGroupId()
java.util.Date	getRunDate()
java.lang.String	getSample()
java.lang.String	getSequencingCenter()
int	hashCode()
void	setDescription(java.lang.String description)
void	setFlowOrder(java.lang.String flowOrder)
void	setKeySequence(java.lang.String keySequence)
void	setLibrary(java.lang.String value)
void	setPlatform(java.lang.String platform)
void	setPlatformModel(java.lang.String platformModel)
void	setPlatformUnit(java.lang.String pu)
void	setPredictedMedianInsertSize(java.lang.Integer predictedMedianInsertSize)
void	setProgramGroup(java.lang.String programGroup)
void	setRunDate(java.util.Date runDate) Converts to Iso8601Date if not already in that form.
void	setSample(java.lang.String value)
void	setSequencingCenter(java.lang.String center)

Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

attributesEqual, attributesHashCode, getAttribute, getAttributes, setAttribute, setAttribute, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

READ_GROUP_ID_TAG

public static final java.lang.String READ_GROUP_ID_TAG

See Also:

Constant Field Values

SEQUENCING_CENTER_TAG

public static final java.lang.String SEQUENCING_CENTER_TAG

See Also:

Constant Field Values

DESCRIPTION_TAG

public static final java.lang.String DESCRIPTION_TAG

See Also:

Constant Field Values

DATE_RUN_PRODUCED_TAG

public static final java.lang.String DATE_RUN_PRODUCED_TAG

See Also:

Constant Field Values

FLOW_ORDER_TAG

public static final java.lang.String FLOW_ORDER_TAG

See Also:

Constant Field Values

KEY_SEQUENCE_TAG

public static final java.lang.String KEY_SEQUENCE_TAG

See Also:

Constant Field Values

LIBRARY_TAG

public static final java.lang.String LIBRARY_TAG

See Also:

Constant Field Values

PROGRAM_GROUP_TAG

public static final java.lang.String PROGRAM_GROUP_TAG

See Also:

Constant Field Values

PREDICTED_MEDIAN_INSERT_SIZE_TAG

public static final java.lang.String PREDICTED_MEDIAN_INSERT_SIZE_TAG

See Also:

Constant Field Values

PLATFORM_TAG

public static final java.lang.String PLATFORM_TAG

See Also:

Constant Field Values

PLATFORM_MODEL_TAG

public static final java.lang.String PLATFORM_MODEL_TAG

See Also:

Constant Field Values

PLATFORM_UNIT_TAG

public static final java.lang.String PLATFORM_UNIT_TAG

See Also:

Constant Field Values

READ_GROUP_SAMPLE_TAG

public static final java.lang.String READ_GROUP_SAMPLE_TAG

See Also:

Constant Field Values

STANDARD_TAGS

public static final java.util.Set<java.lang.String> STANDARD_TAGS

Constructor Detail

SAMReadGroupRecord

public SAMReadGroupRecord(java.lang.String id)

SAMReadGroupRecord

public SAMReadGroupRecord(java.lang.String id,
                  SAMReadGroupRecord srcProgramRecord)

Method Detail

getId

public java.lang.String getId()

Description copied from class: AbstractSAMHeaderRecord

Returns the ID tag (or equivalent) for this header record. The default implementation throws a SAMException to indicate "not implemented".

Overrides:

getId in class AbstractSAMHeaderRecord

getReadGroupId

public java.lang.String getReadGroupId()

getSample

public java.lang.String getSample()

setSample

public void setSample(java.lang.String value)

getLibrary

public java.lang.String getLibrary()

setLibrary

public void setLibrary(java.lang.String value)

getPlatformUnit

public java.lang.String getPlatformUnit()

setPlatformUnit

public void setPlatformUnit(java.lang.String pu)

getPlatform

public java.lang.String getPlatform()

setPlatform

public void setPlatform(java.lang.String platform)

getRunDate

public java.util.Date getRunDate()

getFlowOrder

public java.lang.String getFlowOrder()

setFlowOrder

public void setFlowOrder(java.lang.String flowOrder)

getKeySequence

public java.lang.String getKeySequence()

setKeySequence

public void setKeySequence(java.lang.String keySequence)

setRunDate

public void setRunDate(java.util.Date runDate)

Converts to Iso8601Date if not already in that form.

getSequencingCenter

public java.lang.String getSequencingCenter()

setSequencingCenter

public void setSequencingCenter(java.lang.String center)

getDescription

public java.lang.String getDescription()

setDescription

public void setDescription(java.lang.String description)

getPredictedMedianInsertSize

public java.lang.Integer getPredictedMedianInsertSize()

setPredictedMedianInsertSize

public void setPredictedMedianInsertSize(java.lang.Integer predictedMedianInsertSize)

getProgramGroup

public java.lang.String getProgramGroup()

setProgramGroup

public void setProgramGroup(java.lang.String programGroup)

getPlatformModel

public java.lang.String getPlatformModel()

setPlatformModel

public void setPlatformModel(java.lang.String platformModel)

equivalent

public boolean equivalent(SAMReadGroupRecord that)

Returns:

true if this == that except for the read group ID, which is arbitrary

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object