Package picard.sam.SamErrorMetric
Enum ReadBaseStratification.PairOrientation
- java.lang.Object
-
- java.lang.Enum<ReadBaseStratification.PairOrientation>
-
- picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
-
- All Implemented Interfaces:
Serializable
,Comparable<ReadBaseStratification.PairOrientation>
- Enclosing class:
- ReadBaseStratification
public static enum ReadBaseStratification.PairOrientation extends Enum<ReadBaseStratification.PairOrientation>
An enum for holding a reads read-pair's Orientation (i.e. F1R2, F2R1, or TANDEM) indicating the strand (positive or negative) that each of the two mated reads are aligned to. In connection with READ_BASE and similar stratifiers this can be used to observe oxoG-type sequencing artifacts. Note that this is not related to FR/RF/TANDEM classification as perPairOrientation
.
-
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static ReadBaseStratification.PairOrientation
of(htsjdk.samtools.SAMRecord sam)
static ReadBaseStratification.PairOrientation
valueOf(String name)
Returns the enum constant of this type with the specified name.static ReadBaseStratification.PairOrientation[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
-
-
-
Enum Constant Detail
-
F1R2
public static final ReadBaseStratification.PairOrientation F1R2
-
F2R1
public static final ReadBaseStratification.PairOrientation F2R1
-
F1F2
public static final ReadBaseStratification.PairOrientation F1F2
-
R1R2
public static final ReadBaseStratification.PairOrientation R1R2
-
-
Method Detail
-
values
public static ReadBaseStratification.PairOrientation[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (ReadBaseStratification.PairOrientation c : ReadBaseStratification.PairOrientation.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
-
valueOf
public static ReadBaseStratification.PairOrientation valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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 type has no constant with the specified nameNullPointerException
- if the argument is null
-
of
public static ReadBaseStratification.PairOrientation of(htsjdk.samtools.SAMRecord sam)
-
-