Package htsjdk.samtools

Class SAMReadGroupRecord

java.lang.Object
htsjdk.samtools.AbstractSAMHeaderRecord
htsjdk.samtools.SAMReadGroupRecord
All Implemented Interfaces:
Serializable
public class SAMReadGroupRecord extends AbstractSAMHeaderRecord
Header information about a read group.
See Also:

  • Field Details

  • Constructor Details

    • SAMReadGroupRecord

      public SAMReadGroupRecord(String id)

    • SAMReadGroupRecord

      public SAMReadGroupRecord(String id, SAMReadGroupRecord srcProgramRecord)

  • Method Details

    • 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 class AbstractSAMHeaderRecord

    • getReadGroupId

      public String getReadGroupId()

    • getSample

      public String getSample()

    • setSample

      public void setSample(String value)

    • getLibrary

      public String getLibrary()

    • setLibrary

      public void setLibrary(String value)

    • getPlatformUnit

      public String getPlatformUnit()

    • setPlatformUnit

      public void setPlatformUnit(String pu)

    • getPlatform

      public String getPlatform()

    • setPlatform

      public void setPlatform(String platform)

    • getBarcodes

      public List<String> getBarcodes()
      Returns:
      the List of barcodes associated with this read group or null

    • 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

    • getRunDate

      public Date getRunDate()

    • getFlowOrder

      public String getFlowOrder()

    • setFlowOrder

      public void setFlowOrder(String flowOrder)

    • getKeySequence

      public String getKeySequence()

    • setKeySequence

      public void setKeySequence(String keySequence)

    • setRunDate

      public void setRunDate(Date runDate)
      Converts to Iso8601Date if not already in that form.

    • getSequencingCenter

      public String getSequencingCenter()

    • setSequencingCenter

      public void setSequencingCenter(String center)

    • getDescription

      public String getDescription()

    • setDescription

      public void setDescription(String description)

    • getPredictedMedianInsertSize

      public Integer getPredictedMedianInsertSize()

    • setPredictedMedianInsertSize

      public void setPredictedMedianInsertSize(Integer predictedMedianInsertSize)

    • getProgramGroup

      public String getProgramGroup()

    • setProgramGroup

      public void setProgramGroup(String programGroup)

    • getPlatformModel

      public String getPlatformModel()

    • setPlatformModel

      public void setPlatformModel(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(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • 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 class AbstractSAMHeaderRecord