ReadGroup (Big Data Genomics: Avro Formats 0.15.0 API)

java.lang.Object
- org.apache.avro.specific.SpecificRecordBase
- - org.bdgenomics.formats.avro.ReadGroup

All Implemented Interfaces:

Externalizable, Serializable, Comparable<org.apache.avro.specific.SpecificRecord>, org.apache.avro.generic.GenericContainer, org.apache.avro.generic.GenericRecord, org.apache.avro.generic.IndexedRecord, org.apache.avro.specific.SpecificRecord
```
public class ReadGroup
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
```
See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class ReadGroup.Builder
RecordBuilder for ReadGroup instances.

Nested Classes
Modifier and Type	Class and Description
`static class`	`ReadGroup.Builder` RecordBuilder for ReadGroup instances.

Field Summary

Fields
Modifier and Type	Field and Description
`String`	`description` Deprecated.
`String`	`flowOrder` Deprecated.
`String`	`id` Deprecated.
`String`	`keySequence` Deprecated.
`String`	`library` Deprecated.
`String`	`platform` Deprecated.
`String`	`platformModel` Deprecated.
`String`	`platformUnit` Deprecated.
`Integer`	`predictedMedianInsertSize` Deprecated.
`List<ProcessingStep>`	`processingSteps` Deprecated.
`Long`	`runDateEpoch` Deprecated.
`String`	`sampleId` Deprecated.
`static org.apache.avro.Schema`	`SCHEMA$`
`String`	`sequencingCenter` Deprecated.

Constructor Summary

Constructors
Constructor and Description
`ReadGroup()` Default constructor.
`ReadGroup(String id, String sequencingCenter, String description, Long runDateEpoch, String flowOrder, String keySequence, String library, Integer predictedMedianInsertSize, String platform, String platformModel, String platformUnit, String sampleId, List<ProcessingStep> processingSteps)` All-args constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static org.apache.avro.message.BinaryMessageDecoder<ReadGroup>`	`createDecoder(org.apache.avro.message.SchemaStore resolver)` Create a new BinaryMessageDecoder instance for this class that uses the specified `SchemaStore`.
`static ReadGroup`	`fromByteBuffer(ByteBuffer b)` Deserializes a ReadGroup from a ByteBuffer.
`Object`	`get(int field$)`
`static org.apache.avro.Schema`	`getClassSchema()`
`static org.apache.avro.message.BinaryMessageDecoder<ReadGroup>`	`getDecoder()` Return the BinaryMessageDecoder instance used by this class.
`String`	`getDescription()` Gets the value of the 'description' field.
`String`	`getFlowOrder()` Gets the value of the 'flowOrder' field.
`String`	`getId()` Gets the value of the 'id' field.
`String`	`getKeySequence()` Gets the value of the 'keySequence' field.
`String`	`getLibrary()` Gets the value of the 'library' field.
`String`	`getPlatform()` Gets the value of the 'platform' field.
`String`	`getPlatformModel()` Gets the value of the 'platformModel' field.
`String`	`getPlatformUnit()` Gets the value of the 'platformUnit' field.
`Integer`	`getPredictedMedianInsertSize()` Gets the value of the 'predictedMedianInsertSize' field.
`List<ProcessingStep>`	`getProcessingSteps()` Gets the value of the 'processingSteps' field.
`Long`	`getRunDateEpoch()` Gets the value of the 'runDateEpoch' field.
`String`	`getSampleId()` Gets the value of the 'sampleId' field.
`org.apache.avro.Schema`	`getSchema()`
`String`	`getSequencingCenter()` Gets the value of the 'sequencingCenter' field.
`static ReadGroup.Builder`	`newBuilder()` Creates a new ReadGroup RecordBuilder.
`static ReadGroup.Builder`	`newBuilder(ReadGroup.Builder other)` Creates a new ReadGroup RecordBuilder by copying an existing Builder.
`static ReadGroup.Builder`	`newBuilder(ReadGroup other)` Creates a new ReadGroup RecordBuilder by copying an existing ReadGroup instance.
`void`	`put(int field$, Object value$)`
`void`	`readExternal(ObjectInput in)`
`void`	`setDescription(String value)` Sets the value of the 'description' field.
`void`	`setFlowOrder(String value)` Sets the value of the 'flowOrder' field.
`void`	`setId(String value)` Sets the value of the 'id' field.
`void`	`setKeySequence(String value)` Sets the value of the 'keySequence' field.
`void`	`setLibrary(String value)` Sets the value of the 'library' field.
`void`	`setPlatform(String value)` Sets the value of the 'platform' field.
`void`	`setPlatformModel(String value)` Sets the value of the 'platformModel' field.
`void`	`setPlatformUnit(String value)` Sets the value of the 'platformUnit' field.
`void`	`setPredictedMedianInsertSize(Integer value)` Sets the value of the 'predictedMedianInsertSize' field.
`void`	`setProcessingSteps(List<ProcessingStep> value)` Sets the value of the 'processingSteps' field.
`void`	`setRunDateEpoch(Long value)` Sets the value of the 'runDateEpoch' field.
`void`	`setSampleId(String value)` Sets the value of the 'sampleId' field.
`void`	`setSequencingCenter(String value)` Sets the value of the 'sequencingCenter' field.
`ByteBuffer`	`toByteBuffer()` Serializes this ReadGroup to a ByteBuffer.
`void`	`writeExternal(ObjectOutput out)`

Methods inherited from class org.apache.avro.specific.SpecificRecordBase
compareTo, equals, get, getConverion, getConversion, getConversion, hashCode, put, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - SCHEMA$
```
public static final org.apache.avro.Schema SCHEMA$
```
  - id
```
@Deprecated
public String id
```
    Deprecated.
    
    Read group identifier. SAM tag ID for header record type @RG.
  - sequencingCenter
```
@Deprecated
public String sequencingCenter
```
    Deprecated.
    
    Name of sequencing center producing the reads in this read group. SAM tag CN for header record type @RG.
  - description
```
@Deprecated
public String description
```
    Deprecated.
    
    Description for this read group. SAM tag DS for header record type @RG.
  - runDateEpoch
```
@Deprecated
public Long runDateEpoch
```
    Deprecated.
    
    Date when the sequencing run for this read group was performed. SAM tag DT for header record type @RG.
  - flowOrder
```
@Deprecated
public String flowOrder
```
    Deprecated.
    
    Flow order for the reads in this read group. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. SAM tag FO for header record type @RG. Format (not enforced here): /\*|[ACMGRSVTWYHKDBN]+/
  - keySequence
```
@Deprecated
public String keySequence
```
    Deprecated.
    
    The array of nucleotide bases that correspond to the key sequence of each read in this read group. SAM tag KS for header record type @RG.
  - library
```
@Deprecated
public String library
```
    Deprecated.
    
    Library for this read group. SAM tag LB for header record type @RG.
  - predictedMedianInsertSize
```
@Deprecated
public Integer predictedMedianInsertSize
```
    Deprecated.
    
    Predicted median insert size for this read group. SAM tag PI for header record type @RG.
  - platform
```
@Deprecated
public String platform
```
    Deprecated.
    
    Platform or technology used to produce the reads in this read group. SAM tag PL for header record type @RG. Valid values from the SAM specification (not enforced here): CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, ONT, and PACBIO.
  - platformModel
```
@Deprecated
public String platformModel
```
    Deprecated.
    
    Platform model for this read group, further details of the platform or technology used. SAM tag PM for header record type @RG.
  - platformUnit
```
@Deprecated
public String platformUnit
```
    Deprecated.
    
    Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD) for this read group. SAM tag PU for header record type @RG.
  - sampleId
```
@Deprecated
public String sampleId
```
    Deprecated.
    
    Sample identifier for this read group. Use pool name where a pool is being sequenced. Join with Sample.id for sample metadata. SAM tag SM for header record type @RG.
  - processingSteps
```
@Deprecated
public List<ProcessingStep> processingSteps
```
    Deprecated.
    
    Processing steps that have been applied to this read group. SAM tag PG for header record type @RG.
- Constructor Detail
  - ReadGroup
```
public ReadGroup()
```
    Default constructor. Note that this does not initialize fields to their default values from the schema. If that is desired then one should use newBuilder().
  - ReadGroup
```
public ReadGroup(String id,
                 String sequencingCenter,
                 String description,
                 Long runDateEpoch,
                 String flowOrder,
                 String keySequence,
                 String library,
                 Integer predictedMedianInsertSize,
                 String platform,
                 String platformModel,
                 String platformUnit,
                 String sampleId,
                 List<ProcessingStep> processingSteps)
```
    All-args constructor.
    
    Parameters:
    
    id - Read group identifier. SAM tag ID for header record type @RG.
    
    sequencingCenter - Name of sequencing center producing the reads in this read group. SAM tag CN for header record type @RG.
    
    description - Description for this read group. SAM tag DS for header record type @RG.
    
    runDateEpoch - Date when the sequencing run for this read group was performed. SAM tag DT for header record type @RG.
    
    flowOrder - Flow order for the reads in this read group. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. SAM tag FO for header record type @RG. Format (not enforced here): /\*|[ACMGRSVTWYHKDBN]+/
    
    keySequence - The array of nucleotide bases that correspond to the key sequence of each read in this read group. SAM tag KS for header record type @RG.
    
    library - Library for this read group. SAM tag LB for header record type @RG.
    
    predictedMedianInsertSize - Predicted median insert size for this read group. SAM tag PI for header record type @RG.
    
    platform - Platform or technology used to produce the reads in this read group. SAM tag PL for header record type @RG. Valid values from the SAM specification (not enforced here): CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, ONT, and PACBIO.
    
    platformModel - Platform model for this read group, further details of the platform or technology used. SAM tag PM for header record type @RG.
    
    platformUnit - Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD) for this read group. SAM tag PU for header record type @RG.
    
    sampleId - Sample identifier for this read group. Use pool name where a pool is being sequenced. Join with Sample.id for sample metadata. SAM tag SM for header record type @RG.
    
    processingSteps - Processing steps that have been applied to this read group. SAM tag PG for header record type @RG.
- Method Detail
  - getClassSchema
```
public static org.apache.avro.Schema getClassSchema()
```
  - getDecoder
```
public static org.apache.avro.message.BinaryMessageDecoder<ReadGroup> getDecoder()
```
    Return the BinaryMessageDecoder instance used by this class.
  - createDecoder
```
public static org.apache.avro.message.BinaryMessageDecoder<ReadGroup> createDecoder(org.apache.avro.message.SchemaStore resolver)
```
    Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.
    
    Parameters:
    
    resolver - a SchemaStore used to find schemas by fingerprint
  - toByteBuffer
```
public ByteBuffer toByteBuffer()
                        throws IOException
```
    Serializes this ReadGroup to a ByteBuffer.
    
    Throws:
    
    IOException
  - fromByteBuffer
```
public static ReadGroup fromByteBuffer(ByteBuffer b)
                                throws IOException
```
    Deserializes a ReadGroup from a ByteBuffer.
    
    Throws:
    
    IOException
  - getSchema
```
public org.apache.avro.Schema getSchema()
```
    Specified by:
    
    getSchema in interface org.apache.avro.generic.GenericContainer
    
    Specified by:
    
    getSchema in class org.apache.avro.specific.SpecificRecordBase
  - get
```
public Object get(int field$)
```
    Specified by:
    
    get in interface org.apache.avro.generic.IndexedRecord
    
    Specified by:
    
    get in class org.apache.avro.specific.SpecificRecordBase
  - put
```
public void put(int field$,
                Object value$)
```
    Specified by:
    
    put in interface org.apache.avro.generic.IndexedRecord
    
    Specified by:
    
    put in class org.apache.avro.specific.SpecificRecordBase
  - getId
```
public String getId()
```
    Gets the value of the 'id' field.
    
    Returns:
    
    Read group identifier. SAM tag ID for header record type @RG.
  - setId
```
public void setId(String value)
```
    Sets the value of the 'id' field. Read group identifier. SAM tag ID for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getSequencingCenter
```
public String getSequencingCenter()
```
    Gets the value of the 'sequencingCenter' field.
    
    Returns:
    
    Name of sequencing center producing the reads in this read group. SAM tag CN for header record type @RG.
  - setSequencingCenter
```
public void setSequencingCenter(String value)
```
    Sets the value of the 'sequencingCenter' field. Name of sequencing center producing the reads in this read group. SAM tag CN for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getDescription
```
public String getDescription()
```
    Gets the value of the 'description' field.
    
    Returns:
    
    Description for this read group. SAM tag DS for header record type @RG.
  - setDescription
```
public void setDescription(String value)
```
    Sets the value of the 'description' field. Description for this read group. SAM tag DS for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getRunDateEpoch
```
public Long getRunDateEpoch()
```
    Gets the value of the 'runDateEpoch' field.
    
    Returns:
    
    Date when the sequencing run for this read group was performed. SAM tag DT for header record type @RG.
  - setRunDateEpoch
```
public void setRunDateEpoch(Long value)
```
    Sets the value of the 'runDateEpoch' field. Date when the sequencing run for this read group was performed. SAM tag DT for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getFlowOrder
```
public String getFlowOrder()
```
    Gets the value of the 'flowOrder' field.
    
    Returns:
    
    Flow order for the reads in this read group. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. SAM tag FO for header record type @RG. Format (not enforced here): /\*|[ACMGRSVTWYHKDBN]+/
  - setFlowOrder
```
public void setFlowOrder(String value)
```
    Sets the value of the 'flowOrder' field. Flow order for the reads in this read group. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. SAM tag FO for header record type @RG. Format (not enforced here): /\*|[ACMGRSVTWYHKDBN]+/
    
    Parameters:
    
    value - the value to set.
  - getKeySequence
```
public String getKeySequence()
```
    Gets the value of the 'keySequence' field.
    
    Returns:
    
    The array of nucleotide bases that correspond to the key sequence of each read in this read group. SAM tag KS for header record type @RG.
  - setKeySequence
```
public void setKeySequence(String value)
```
    Sets the value of the 'keySequence' field. The array of nucleotide bases that correspond to the key sequence of each read in this read group. SAM tag KS for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getLibrary
```
public String getLibrary()
```
    Gets the value of the 'library' field.
    
    Returns:
    
    Library for this read group. SAM tag LB for header record type @RG.
  - setLibrary
```
public void setLibrary(String value)
```
    Sets the value of the 'library' field. Library for this read group. SAM tag LB for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getPredictedMedianInsertSize
```
public Integer getPredictedMedianInsertSize()
```
    Gets the value of the 'predictedMedianInsertSize' field.
    
    Returns:
    
    Predicted median insert size for this read group. SAM tag PI for header record type @RG.
  - setPredictedMedianInsertSize
```
public void setPredictedMedianInsertSize(Integer value)
```
    Sets the value of the 'predictedMedianInsertSize' field. Predicted median insert size for this read group. SAM tag PI for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getPlatform
```
public String getPlatform()
```
    Gets the value of the 'platform' field.
    
    Returns:
    
    Platform or technology used to produce the reads in this read group. SAM tag PL for header record type @RG. Valid values from the SAM specification (not enforced here): CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, ONT, and PACBIO.
  - setPlatform
```
public void setPlatform(String value)
```
    Sets the value of the 'platform' field. Platform or technology used to produce the reads in this read group. SAM tag PL for header record type @RG. Valid values from the SAM specification (not enforced here): CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, ONT, and PACBIO.
    
    Parameters:
    
    value - the value to set.
  - getPlatformModel
```
public String getPlatformModel()
```
    Gets the value of the 'platformModel' field.
    
    Returns:
    
    Platform model for this read group, further details of the platform or technology used. SAM tag PM for header record type @RG.
  - setPlatformModel
```
public void setPlatformModel(String value)
```
    Sets the value of the 'platformModel' field. Platform model for this read group, further details of the platform or technology used. SAM tag PM for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getPlatformUnit
```
public String getPlatformUnit()
```
    Gets the value of the 'platformUnit' field.
    
    Returns:
    
    Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD) for this read group. SAM tag PU for header record type @RG.
  - setPlatformUnit
```
public void setPlatformUnit(String value)
```
    Sets the value of the 'platformUnit' field. Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD) for this read group. SAM tag PU for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getSampleId
```
public String getSampleId()
```
    Gets the value of the 'sampleId' field.
    
    Returns:
    
    Sample identifier for this read group. Use pool name where a pool is being sequenced. Join with Sample.id for sample metadata. SAM tag SM for header record type @RG.
  - setSampleId
```
public void setSampleId(String value)
```
    Sets the value of the 'sampleId' field. Sample identifier for this read group. Use pool name where a pool is being sequenced. Join with Sample.id for sample metadata. SAM tag SM for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - getProcessingSteps
```
public List<ProcessingStep> getProcessingSteps()
```
    Gets the value of the 'processingSteps' field.
    
    Returns:
    
    Processing steps that have been applied to this read group. SAM tag PG for header record type @RG.
  - setProcessingSteps
```
public void setProcessingSteps(List<ProcessingStep> value)
```
    Sets the value of the 'processingSteps' field. Processing steps that have been applied to this read group. SAM tag PG for header record type @RG.
    
    Parameters:
    
    value - the value to set.
  - newBuilder
```
public static ReadGroup.Builder newBuilder()
```
    Creates a new ReadGroup RecordBuilder.
    
    Returns:
    
    A new ReadGroup RecordBuilder
  - newBuilder
```
public static ReadGroup.Builder newBuilder(ReadGroup.Builder other)
```
    Creates a new ReadGroup RecordBuilder by copying an existing Builder.
    
    Parameters:
    
    other - The existing builder to copy.
    
    Returns:
    
    A new ReadGroup RecordBuilder
  - newBuilder
```
public static ReadGroup.Builder newBuilder(ReadGroup other)
```
    Creates a new ReadGroup RecordBuilder by copying an existing ReadGroup instance.
    
    Parameters:
    
    other - The existing instance to copy.
    
    Returns:
    
    A new ReadGroup RecordBuilder
  - writeExternal
```
public void writeExternal(ObjectOutput out)
                   throws IOException
```
    Specified by:
    
    writeExternal in interface Externalizable
    
    Overrides:
    
    writeExternal in class org.apache.avro.specific.SpecificRecordBase
    
    Throws:
    
    IOException
  - readExternal
```
public void readExternal(ObjectInput in)
                  throws IOException
```
    Specified by:
    
    readExternal in interface Externalizable
    
    Overrides:
    
    readExternal in class org.apache.avro.specific.SpecificRecordBase
    
    Throws:
    
    IOException

Class ReadGroup

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.apache.avro.specific.SpecificRecordBase

Methods inherited from class java.lang.Object

Field Detail

SCHEMA$

id

sequencingCenter

description

runDateEpoch

flowOrder

keySequence

library

predictedMedianInsertSize

platform

platformModel

platformUnit

sampleId

processingSteps

Constructor Detail

ReadGroup

ReadGroup

Method Detail

getClassSchema

getDecoder

createDecoder

toByteBuffer

fromByteBuffer

getSchema

get

put

getId

setId

getSequencingCenter

setSequencingCenter

getDescription

setDescription

getRunDateEpoch

setRunDateEpoch

getFlowOrder

setFlowOrder

getKeySequence

setKeySequence

getLibrary

setLibrary

getPredictedMedianInsertSize

setPredictedMedianInsertSize

getPlatform

setPlatform

getPlatformModel

setPlatformModel

getPlatformUnit

setPlatformUnit

getSampleId

setSampleId

getProcessingSteps

setProcessingSteps

newBuilder

newBuilder

newBuilder

writeExternal

readExternal