htsjdk.samtools

Enum SamFlagField

java.lang.Object

java.lang.Enum<SamFlagField>

htsjdk.samtools.SamFlagField

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<SamFlagField>

public enum SamFlagField
extends java.lang.Enum<SamFlagField>

This determines how flag fields are represented in the SAM file. In a string FLAG, each character represents one bit with p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped), U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse) 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), x=0x200 (failure), d=0x400 (duplicate), and S=0x800 (secondary). This was inspired by 'samtools view -X'. We also output a character when the following bits *are not* set: m=0x4 (mapped), M=0x8 (mate mapped), f=0x10 (forward), F=0x20 (mate forward).

Enum Constant Summary

Enum Constants

Enum Constant and Description
DECIMAL
HEXADECIMAL
NONE
OCTAL
STRING

Method Summary

Modifier and Type	Method and Description
abstract java.lang.String	format(int flag) Returns the string associated with this flag field.
static SamFlagField	of(java.lang.String s) Returns the type of flag field for this string.
int	parse(java.lang.String flag) Parses the flag.
static int	parseDefault(java.lang.String flag) Infers the format from the flag string and parses the flag.
protected abstract int	parseWithoutValidation(java.lang.String flag) Performs the actual parsing based on the radix.
static SamFlagField	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static SamFlagField[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

NONE

public static final SamFlagField NONE

DECIMAL

public static final SamFlagField DECIMAL

HEXADECIMAL

public static final SamFlagField HEXADECIMAL

OCTAL

public static final SamFlagField OCTAL

STRING

public static final SamFlagField STRING

Method Detail

values

public static SamFlagField[] 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 (SamFlagField c : SamFlagField.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static SamFlagField valueOf(java.lang.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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

format

public abstract java.lang.String format(int flag)

Returns the string associated with this flag field.

parse

public final int parse(java.lang.String flag)

Parses the flag. Validates that the flag is of the correct type.

parseDefault

public static int parseDefault(java.lang.String flag)

Infers the format from the flag string and parses the flag.

parseWithoutValidation

protected abstract int parseWithoutValidation(java.lang.String flag)

Performs the actual parsing based on the radix. No validation that the flag is of the correct radix should be performed.

of

public static SamFlagField of(java.lang.String s)

Returns the type of flag field for this string. This does not guarantee it is of the flag field, as it only checks the first two characters.