Package htsjdk.samtools

Class SAMProgramRecord

java.lang.Object
htsjdk.samtools.AbstractSAMHeaderRecord
htsjdk.samtools.SAMProgramRecord
All Implemented Interfaces:
Serializable
public class SAMProgramRecord extends AbstractSAMHeaderRecord
In-memory representation of @PG SAM header record.
See Also:

  • Field Details

  • Constructor Details

    • SAMProgramRecord

      public SAMProgramRecord(String programGroupId)

    • SAMProgramRecord

      public SAMProgramRecord(String id, SAMProgramRecord 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

    • getProgramGroupId

      public String getProgramGroupId()

    • getProgramName

      public String getProgramName()

    • setProgramName

      public void setProgramName(String name)

    • getProgramVersion

      public String getProgramVersion()

    • setProgramVersion

      public void setProgramVersion(String version)

    • getCommandLine

      public String getCommandLine()

    • setCommandLine

      public void setCommandLine(String commandLine)

    • getPreviousProgramGroupId

      public String getPreviousProgramGroupId()

    • setPreviousProgramGroupId

      public void setPreviousProgramGroupId(String id)

    • equivalent

      public boolean equivalent(SAMProgramRecord that)
      Returns:
      true if this == that except for the program 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