htsjdk.samtools.cram.structure

Class CramCompressionRecord.BAM_FLAGS

java.lang.Object

htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS

Enclosing class:

CramCompressionRecord

public static class CramCompressionRecord.BAM_FLAGS
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	DUPLICATE_READ_FLAG
static int	FIRST_OF_PAIR_FLAG
static int	MATE_STRAND_FLAG
static int	MATE_UNMAPPED_FLAG
static int	NOT_PRIMARY_ALIGNMENT_FLAG
static int	PROPER_PAIR_FLAG
static int	READ_FAILS_VENDOR_QUALITY_CHECK_FLAG
static int	READ_PAIRED_FLAG
static int	READ_STRAND_FLAG
static int	READ_UNMAPPED_FLAG
static int	SECOND_OF_PAIR_FLAG
static int	SUPPLEMENTARY_FLAG

Constructor Summary

Constructors

Constructor and Description
BAM_FLAGS()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

READ_PAIRED_FLAG

public static final int READ_PAIRED_FLAG

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Constant Field Values

PROPER_PAIR_FLAG

public static final int PROPER_PAIR_FLAG

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Constant Field Values

READ_UNMAPPED_FLAG

public static final int READ_UNMAPPED_FLAG

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Constant Field Values

MATE_UNMAPPED_FLAG

public static final int MATE_UNMAPPED_FLAG

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Constant Field Values

READ_STRAND_FLAG

public static final int READ_STRAND_FLAG

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Constant Field Values

MATE_STRAND_FLAG

public static final int MATE_STRAND_FLAG

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Constant Field Values

FIRST_OF_PAIR_FLAG

public static final int FIRST_OF_PAIR_FLAG

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Constant Field Values

SECOND_OF_PAIR_FLAG

public static final int SECOND_OF_PAIR_FLAG

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Constant Field Values

NOT_PRIMARY_ALIGNMENT_FLAG

public static final int NOT_PRIMARY_ALIGNMENT_FLAG

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Constant Field Values

READ_FAILS_VENDOR_QUALITY_CHECK_FLAG

public static final int READ_FAILS_VENDOR_QUALITY_CHECK_FLAG

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Constant Field Values

DUPLICATE_READ_FLAG

public static final int DUPLICATE_READ_FLAG

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Constant Field Values

SUPPLEMENTARY_FLAG

public static final int SUPPLEMENTARY_FLAG

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Constant Field Values

Constructor Detail

BAM_FLAGS

public BAM_FLAGS()