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:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	SAMValidationError.Severity
static enum	SAMValidationError.Type

Field Summary

Fields

Modifier and Type	Field	Description
static final long	serialVersionUID

Constructor Summary

Constructors

Constructor	Description
SAMValidationError(SAMValidationError.Type type, String message, String readName)	Construct a SAMValidationError with unknown record number.
SAMValidationError(SAMValidationError.Type type, String message, String readName, long recordNumber)	Construct a SAMValidationError with possibly-known record number.

Method Summary

Modifier and Type	Method	Description
String	getMessage()
String	getReadName()	may be null
long	getRecordNumber()	1-based.
String	getSource()
SAMValidationError.Type	getType()
void	setRecordNumber(long recordNumber)
void	setSource(String source)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

serialVersionUID

public static final long serialVersionUID

See Also:

• Constant Field Values

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)