org.utgenome.gwt.utgb.client.bio
Class SAMReadFlag

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.SAMReadFlag

public class SAMReadFlag
extends Object

Flag bits of SAM reads

Author:

leo

Field Summary

static int	FLAG_FAILS_QUALITY_CHECK
static int	FLAG_IS_FIRST_READ
static int	FLAG_IS_SECOND_READ
static int	FLAG_MAPPED_IN_A_PROPER_PAIR
static int	FLAG_MATE_IS_UNMAPPED
static int	FLAG_NOT_PRIMARY
static int	FLAG_PAIRED_READ
static int	FLAG_PCR_OR_OPTICAL_DUPLICATE
static int	FLAG_QUERY_IS_UNMAPPED
static int	FLAG_STRAND_OF_MATE
static int	FLAG_STRAND_OF_QUERY

Constructor Summary

SAMReadFlag()

Method Summary

static boolean	isFirstRead(int flag)
static boolean	isMappedInProperPair(int flag)
static boolean	isMateForwardStrand(int flag)
static boolean	isMateUnmapped(int flag)
static boolean	isPairedRead(int flag)
static boolean	isQueryForwardStrand(int flag)
static boolean	isQueryUnmapped(int flag)
static boolean	isSecondRead(int flag)

Methods inherited from class java.lang.Object

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

Field Detail

FLAG_PAIRED_READ

public static final int FLAG_PAIRED_READ

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Constant Field Values

FLAG_MAPPED_IN_A_PROPER_PAIR

public static final int FLAG_MAPPED_IN_A_PROPER_PAIR

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Constant Field Values

FLAG_QUERY_IS_UNMAPPED

public static final int FLAG_QUERY_IS_UNMAPPED

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Constant Field Values

FLAG_MATE_IS_UNMAPPED

public static final int FLAG_MATE_IS_UNMAPPED

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Constant Field Values

FLAG_STRAND_OF_QUERY

public static final int FLAG_STRAND_OF_QUERY

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Constant Field Values

FLAG_STRAND_OF_MATE

public static final int FLAG_STRAND_OF_MATE

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Constant Field Values

FLAG_IS_FIRST_READ

public static final int FLAG_IS_FIRST_READ

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Constant Field Values

FLAG_IS_SECOND_READ

public static final int FLAG_IS_SECOND_READ

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Constant Field Values

FLAG_NOT_PRIMARY

public static final int FLAG_NOT_PRIMARY

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Constant Field Values

FLAG_FAILS_QUALITY_CHECK

public static final int FLAG_FAILS_QUALITY_CHECK

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Constant Field Values

FLAG_PCR_OR_OPTICAL_DUPLICATE

public static final int FLAG_PCR_OR_OPTICAL_DUPLICATE

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Constant Field Values

Constructor Detail

SAMReadFlag

public SAMReadFlag()

Method Detail

isPairedRead

public static boolean isPairedRead(int flag)

isMappedInProperPair

public static boolean isMappedInProperPair(int flag)

isQueryUnmapped

public static boolean isQueryUnmapped(int flag)

isMateUnmapped

public static boolean isMateUnmapped(int flag)

isQueryForwardStrand

public static boolean isQueryForwardStrand(int flag)

isMateForwardStrand

public static boolean isMateForwardStrand(int flag)

isFirstRead

public static boolean isFirstRead(int flag)

isSecondRead

public static boolean isSecondRead(int flag)