Class Substitution
- java.lang.Object
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- htsjdk.samtools.cram.encoding.readfeatures.Substitution
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- All Implemented Interfaces:
ReadFeature
,Serializable
public class Substitution extends Object implements Serializable, ReadFeature
A substitution event captured in read coordinates. It is characterized by position in read, read base and reference base. The class is also responsible for converting combinations of read base and reference base into a byte value (code). Both reference and read bases must be ACGTN only.- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description Substitution(int position, byte code)
Substitution(int position, byte base, byte referenceBase)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
equals(Object obj)
byte
getBase()
byte
getCode()
byte
getOperator()
Read features are distinguished by operator, similar to cigar operator.int
getPosition()
byte
getReferenceBase()
int
hashCode()
void
setCode(byte code)
String
toString()
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Field Detail
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NO_CODE
public static final int NO_CODE
- See Also:
- Constant Field Values
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operator
public static final byte operator
- See Also:
- Constant Field Values
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Method Detail
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getCode
public byte getCode()
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setCode
public void setCode(byte code)
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getOperator
public byte getOperator()
Description copied from interface:ReadFeature
Read features are distinguished by operator, similar to cigar operator.- Specified by:
getOperator
in interfaceReadFeature
- Returns:
- type of the read feature
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getPosition
public int getPosition()
- Specified by:
getPosition
in interfaceReadFeature
- Returns:
- zero-based position in the read
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getBase
public byte getBase()
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getReferenceBase
public byte getReferenceBase()
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