Package htsjdk.samtools
Class SAMReadGroupRecord
- java.lang.Object
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- htsjdk.samtools.AbstractSAMHeaderRecord
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- htsjdk.samtools.SAMReadGroupRecord
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- All Implemented Interfaces:
Serializable
public class SAMReadGroupRecord extends AbstractSAMHeaderRecord
Header information about a read group.- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SAMReadGroupRecord.PlatformValue
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Field Summary
Fields Modifier and Type Field Description static String
BARCODE_TAG
static String
DATE_RUN_PRODUCED_TAG
static String
DESCRIPTION_TAG
static String
FLOW_ORDER_TAG
static String
KEY_SEQUENCE_TAG
static String
LIBRARY_TAG
static String
PLATFORM_MODEL_TAG
static String
PLATFORM_TAG
static String
PLATFORM_UNIT_TAG
static String
PREDICTED_MEDIAN_INSERT_SIZE_TAG
static String
PROGRAM_GROUP_TAG
static String
READ_GROUP_ID_TAG
static String
READ_GROUP_SAMPLE_TAG
static String
SEQUENCING_CENTER_TAG
static Set<String>
STANDARD_TAGS
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Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord
serialVersionUID
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Constructor Summary
Constructors Constructor Description SAMReadGroupRecord(String id)
SAMReadGroupRecord(String id, SAMReadGroupRecord srcProgramRecord)
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Method Summary
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Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord
attributesEqual, attributesHashCode, getAttribute, getAttributes, setAttribute, setAttribute, setAttribute, toString
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Field Detail
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READ_GROUP_ID_TAG
public static final String READ_GROUP_ID_TAG
- See Also:
- Constant Field Values
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SEQUENCING_CENTER_TAG
public static final String SEQUENCING_CENTER_TAG
- See Also:
- Constant Field Values
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DESCRIPTION_TAG
public static final String DESCRIPTION_TAG
- See Also:
- Constant Field Values
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DATE_RUN_PRODUCED_TAG
public static final String DATE_RUN_PRODUCED_TAG
- See Also:
- Constant Field Values
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FLOW_ORDER_TAG
public static final String FLOW_ORDER_TAG
- See Also:
- Constant Field Values
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KEY_SEQUENCE_TAG
public static final String KEY_SEQUENCE_TAG
- See Also:
- Constant Field Values
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LIBRARY_TAG
public static final String LIBRARY_TAG
- See Also:
- Constant Field Values
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PROGRAM_GROUP_TAG
public static final String PROGRAM_GROUP_TAG
- See Also:
- Constant Field Values
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PREDICTED_MEDIAN_INSERT_SIZE_TAG
public static final String PREDICTED_MEDIAN_INSERT_SIZE_TAG
- See Also:
- Constant Field Values
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PLATFORM_TAG
public static final String PLATFORM_TAG
- See Also:
- Constant Field Values
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PLATFORM_MODEL_TAG
public static final String PLATFORM_MODEL_TAG
- See Also:
- Constant Field Values
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PLATFORM_UNIT_TAG
public static final String PLATFORM_UNIT_TAG
- See Also:
- Constant Field Values
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READ_GROUP_SAMPLE_TAG
public static final String READ_GROUP_SAMPLE_TAG
- See Also:
- Constant Field Values
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BARCODE_TAG
public static final String BARCODE_TAG
- See Also:
- Constant Field Values
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Constructor Detail
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SAMReadGroupRecord
public SAMReadGroupRecord(String id)
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SAMReadGroupRecord
public SAMReadGroupRecord(String id, SAMReadGroupRecord srcProgramRecord)
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Method Detail
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getId
public 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 classAbstractSAMHeaderRecord
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getReadGroupId
public String getReadGroupId()
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getSample
public String getSample()
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setSample
public void setSample(String value)
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getLibrary
public String getLibrary()
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setLibrary
public void setLibrary(String value)
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getPlatformUnit
public String getPlatformUnit()
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setPlatformUnit
public void setPlatformUnit(String pu)
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getPlatform
public String getPlatform()
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setPlatform
public void setPlatform(String platform)
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getBarcodes
public List<String> getBarcodes()
- Returns:
- the List of barcodes associated with this read group or null
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setBarcodes
public void setBarcodes(List<String> barcodes)
Set the barcodes associated with this ReadGroup. Note that an input of null results in unsetting the attribute while an empty list is set as a tag with an empty value.- Parameters:
barcodes
- a list of barcodes to associate with this read group
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getRunDate
public Date getRunDate()
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getFlowOrder
public String getFlowOrder()
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setFlowOrder
public void setFlowOrder(String flowOrder)
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getKeySequence
public String getKeySequence()
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setKeySequence
public void setKeySequence(String keySequence)
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setRunDate
public void setRunDate(Date runDate)
Converts to Iso8601Date if not already in that form.
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getSequencingCenter
public String getSequencingCenter()
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setSequencingCenter
public void setSequencingCenter(String center)
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getDescription
public String getDescription()
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setDescription
public void setDescription(String description)
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getPredictedMedianInsertSize
public Integer getPredictedMedianInsertSize()
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setPredictedMedianInsertSize
public void setPredictedMedianInsertSize(Integer predictedMedianInsertSize)
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getProgramGroup
public String getProgramGroup()
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setProgramGroup
public void setProgramGroup(String programGroup)
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getPlatformModel
public String getPlatformModel()
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setPlatformModel
public void setPlatformModel(String platformModel)
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equivalent
public boolean equivalent(SAMReadGroupRecord that)
- Returns:
- true if this == that except for the read group ID, which is arbitrary
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getSAMString
public String getSAMString()
Description copied from class:AbstractSAMHeaderRecord
Returns the record in the SAM line-based text format. Fields are separated by '\t' characters. The String is NOT terminated by '\n'.- Specified by:
getSAMString
in classAbstractSAMHeaderRecord
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