htsjdk.samtools.cram.structure

Enum DataSeries

java.lang.Object

java.lang.Enum<DataSeries>

htsjdk.samtools.cram.structure.DataSeries

All Implemented Interfaces:

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

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

Represents a specific CRAM record data series and its associated type and unique Content ID

Enum Constant Summary

Enum Constants

Enum Constant and Description
AP_AlignmentPositionOffset
BA_Base
BB_bases
BF_BitFlags
BS_BaseSubstitutionCode
CF_CompressionBitFlags
DL_DeletionLength
FC_FeatureCode
FN_NumberOfReadFeatures
FP_FeaturePosition
HC_HardClip
IN_Insertion
MF_MateBitFlags
MQ_MappingQualityScore
NF_RecordsToNextFragment
NP_NextFragmentAlignmentStart
NS_NextFragmentReferenceSequenceID
PD_padding
QQ_scores
QS_QualityScore
RG_ReadGroup
RI_RefId
RL_ReadLength
RN_ReadName
RS_RefSkip
SC_SoftClip
TC_TagCount
TL_TagIdList
TM_TestMark
TN_TagNameAndType
TS_InsertSize
TV_TestMark

Method Summary

Modifier and Type	Method and Description
static DataSeries	byCanonicalName(java.lang.String dataSeriesAbbreviation) Return the DataSeries associated with the two-character canonical name
java.lang.String	getCanonicalName()
java.lang.Integer	getExternalBlockContentId()
DataSeriesType	getType()
static DataSeries	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static DataSeries[]	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

BF_BitFlags

public static final DataSeries BF_BitFlags

CF_CompressionBitFlags

public static final DataSeries CF_CompressionBitFlags

RI_RefId

public static final DataSeries RI_RefId

RL_ReadLength

public static final DataSeries RL_ReadLength

AP_AlignmentPositionOffset

public static final DataSeries AP_AlignmentPositionOffset

RG_ReadGroup

public static final DataSeries RG_ReadGroup

RN_ReadName

public static final DataSeries RN_ReadName

NF_RecordsToNextFragment

public static final DataSeries NF_RecordsToNextFragment

MF_MateBitFlags

public static final DataSeries MF_MateBitFlags

NS_NextFragmentReferenceSequenceID

public static final DataSeries NS_NextFragmentReferenceSequenceID

NP_NextFragmentAlignmentStart

public static final DataSeries NP_NextFragmentAlignmentStart

TS_InsertSize

public static final DataSeries TS_InsertSize

TL_TagIdList

public static final DataSeries TL_TagIdList

TC_TagCount

public static final DataSeries TC_TagCount

TN_TagNameAndType

public static final DataSeries TN_TagNameAndType

MQ_MappingQualityScore

public static final DataSeries MQ_MappingQualityScore

FN_NumberOfReadFeatures

public static final DataSeries FN_NumberOfReadFeatures

FP_FeaturePosition

public static final DataSeries FP_FeaturePosition

FC_FeatureCode

public static final DataSeries FC_FeatureCode

BB_bases

public static final DataSeries BB_bases

QQ_scores

public static final DataSeries QQ_scores

BA_Base

public static final DataSeries BA_Base

QS_QualityScore

public static final DataSeries QS_QualityScore

BS_BaseSubstitutionCode

public static final DataSeries BS_BaseSubstitutionCode

IN_Insertion

public static final DataSeries IN_Insertion

DL_DeletionLength

public static final DataSeries DL_DeletionLength

RS_RefSkip

public static final DataSeries RS_RefSkip

SC_SoftClip

public static final DataSeries SC_SoftClip

PD_padding

public static final DataSeries PD_padding

HC_HardClip

public static final DataSeries HC_HardClip

TM_TestMark

public static final DataSeries TM_TestMark

TV_TestMark

public static final DataSeries TV_TestMark

Method Detail

values

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

Returns:

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

valueOf

public static DataSeries 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

getType

public DataSeriesType getType()

getCanonicalName

public java.lang.String getCanonicalName()

getExternalBlockContentId

public java.lang.Integer getExternalBlockContentId()

byCanonicalName

public static DataSeries byCanonicalName(java.lang.String dataSeriesAbbreviation)

Return the DataSeries associated with the two-character canonical name

Parameters:

dataSeriesAbbreviation - A Data Series canonical name, such as QS for Quality Score

Returns:

the associated DataSeries

Throws:

CRAMException - for an unknown Data Series