Package htsjdk.samtools
Enum Class SAMFlag
- All Implemented Interfaces:
Serializable
,Comparable<SAMFlag>
,Constable
SAM flags as enum, to be used in GUI, menu, etc...
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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 -
Method Summary
Modifier and TypeMethodDescriptionstatic SAMFlag
findByName
(String flag) getFlags
(int flag) getLabel()
int
intValue()
boolean
isSet
(int flag) boolean
isUnset
(int flag) static SAMFlag
valueOf
(int flag) Returns the enum constant of this class with the specified name.static SAMFlag
Returns the enum constant of this class with the specified name.static SAMFlag[]
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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READ_PAIRED
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PROPER_PAIR
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READ_UNMAPPED
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MATE_UNMAPPED
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READ_REVERSE_STRAND
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MATE_REVERSE_STRAND
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FIRST_OF_PAIR
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SECOND_OF_PAIR
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SECONDARY_ALIGNMENT
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NOT_PRIMARY_ALIGNMENT
Deprecated.useSECONDARY_ALIGNMENT
instead. -
READ_FAILS_VENDOR_QUALITY_CHECK
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DUPLICATE_READ
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SUPPLEMENTARY_ALIGNMENT
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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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intValue
public int intValue()- Returns:
- this flag as an int
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getLabel
- Returns:
- a human label for this SAMFlag
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getDescription
- Returns:
- a human description for this SAMFlag
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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:
flag
- 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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findByName
- Returns:
- find SAMFlag the flag by name, or null if it was not found
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isSet
public boolean isSet(int flag) -
isUnset
public boolean isUnset(int flag) -
getFlags
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SECONDARY_ALIGNMENT
instead.