Package htsjdk.samtools

Class SAMValidationError

java.lang.Object
htsjdk.samtools.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:

  • Field Details

  • Constructor Details

    • 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 Details

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getType

      public SAMValidationError.Type getType()

    • 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)