Package htsjdk.samtools
Enum Class CigarOperator
- All Implemented Interfaces:
Serializable
,Comparable<CigarOperator>
,Constable
The operators that can appear in a cigar string, and information about their disk representations.
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum Constants -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final CigarOperator
static final CigarOperator
static final CigarOperator
static final CigarOperator
static final CigarOperator
static final CigarOperator
static final CigarOperator
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Method Summary
Modifier and TypeMethodDescriptionstatic CigarOperator
binaryToEnum
(int i) static CigarOperator
characterToEnum
(int b) boolean
If true, represents that this cigar operator "consumes" bases from the read bases.boolean
If true, represents that this cigar operator "consumes" bases from the reference sequence.static int
static byte
Returns the character that should be used within a SAM file.boolean
Returns true if the operator is a M, a X or a EQboolean
Returns true if the operator is a clipped (hard or soft) operatorboolean
isIndel()
Returns true if the operator is a Insertion or Deletion operatorboolean
Returns true if the operator is a Skipped Region Insertion or Deletion operatorboolean
Returns true if the operator is a Padding operatortoString()
Returns the cigar operator as it would be seen in a SAM file.static CigarOperator
Returns the enum constant of this class with the specified name.static CigarOperator[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.
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Enum Constant Details
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M
Match or mismatch -
I
Insertion vs. the reference. -
D
Deletion vs. the reference. -
N
Skipped region from the reference. -
S
Soft clip. -
H
Hard clip. -
P
Padding. -
EQ
Matches the reference. -
X
Mismatches the reference.
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Field Details
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MATCH_OR_MISMATCH
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INSERTION
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DELETION
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SKIPPED_REGION
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SOFT_CLIP
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HARD_CLIP
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PADDING
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Method Details
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values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
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valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum class has no constant with the specified nameNullPointerException
- if the argument is null
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consumesReadBases
public boolean consumesReadBases()If true, represents that this cigar operator "consumes" bases from the read bases. -
consumesReferenceBases
public boolean consumesReferenceBases()If true, represents that this cigar operator "consumes" bases from the reference sequence. -
characterToEnum
- Parameters:
b
- CIGAR operator in character form as appears in a text CIGAR string- Returns:
- CigarOperator enum value corresponding to the given character.
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binaryToEnum
- Parameters:
i
- CIGAR operator in binary form as appears in a BAMRecord.- Returns:
- CigarOperator enum value corresponding to the given int value.
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enumToBinary
- Parameters:
e
- CigarOperator enum value.- Returns:
- CIGAR operator corresponding to the enum value in binary form as appears in a BAMRecord.
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enumToCharacter
Returns the character that should be used within a SAM file. -
isClipping
public boolean isClipping()Returns true if the operator is a clipped (hard or soft) operator -
isIndel
public boolean isIndel()Returns true if the operator is a Insertion or Deletion operator -
isIndelOrSkippedRegion
public boolean isIndelOrSkippedRegion()Returns true if the operator is a Skipped Region Insertion or Deletion operator -
isAlignment
public boolean isAlignment()Returns true if the operator is a M, a X or a EQ -
isPadding
public boolean isPadding()Returns true if the operator is a Padding operator -
toString
Returns the cigar operator as it would be seen in a SAM file.- Overrides:
toString
in classEnum<CigarOperator>
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