SAMValidationError (htsjdk 2.24.1 API)

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 class SAMValidationError.Severity

static class SAMValidationError.Type

Field Summary

Fields
Modifier and Type Field Description

static 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

All Methods Instance Methods Concrete Methods
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 Detail
- serialVersionUID
```
public static final long serialVersionUID
```
  See Also:
  
  Constant Field Values

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

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)