Class SAMValidationError

  • All Implemented Interfaces:
    Serializable

    public class SAMValidationError
    extends Object
    implements Serializable
    Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type.
    See Also:
    Serialized Form
    • Constructor Detail

      • SAMValidationError

        public SAMValidationError​(SAMValidationError.Type type,
                                  String message,
                                  String readName)
        Construct a SAMValidationError with unknown record number.
        Parameters:
        type -
        message -
        readName - May be null if readName is not known.
      • SAMValidationError

        public SAMValidationError​(SAMValidationError.Type type,
                                  String message,
                                  String readName,
                                  long recordNumber)
        Construct a SAMValidationError with possibly-known record number.
        Parameters:
        type - The validation error type
        message - The message explaining the problem
        readName - The read which is the cause of the violation. May be null if readName is not known.
        recordNumber - Position of the record in the SAM file it has been read from. -1 if not known.
    • Method Detail

      • getMessage

        public String getMessage()
      • getReadName

        public String getReadName()
        may be null
      • getRecordNumber

        public long getRecordNumber()
        1-based. -1 if not known.
      • setRecordNumber

        public void setRecordNumber​(long recordNumber)
      • getSource

        public String getSource()
      • setSource

        public void setSource​(String source)