Package htsjdk.samtools
Class SAMValidationError
- java.lang.Object
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- htsjdk.samtools.SAMValidationError
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- 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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SAMValidationError.Severity
static class
SAMValidationError.Type
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Field Summary
Fields Modifier and Type Field Description static long
serialVersionUID
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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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getMessage()
String
getReadName()
may be nulllong
getRecordNumber()
1-based.String
getSource()
SAMValidationError.Type
getType()
void
setRecordNumber(long recordNumber)
void
setSource(String source)
String
toString()
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Field Detail
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serialVersionUID
public static final long serialVersionUID
- See Also:
- Constant Field Values
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Constructor Detail
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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.
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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 typemessage
- The message explaining the problemreadName
- 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.
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Method Detail
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getType
public SAMValidationError.Type getType()
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getMessage
public String getMessage()
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getReadName
public String getReadName()
may be null
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getRecordNumber
public long getRecordNumber()
1-based. -1 if not known.
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setRecordNumber
public void setRecordNumber(long recordNumber)
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getSource
public String getSource()
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setSource
public void setSource(String source)
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