Package htsjdk.samtools.cram.structure
Enum DataSeries
- java.lang.Object
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- java.lang.Enum<DataSeries>
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- htsjdk.samtools.cram.structure.DataSeries
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- All Implemented Interfaces:
Serializable
,Comparable<DataSeries>
public enum DataSeries extends Enum<DataSeries>
Represents a specific CRAM record data series and its associated type and unique Content ID
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Enum Constant Summary
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static DataSeries
byCanonicalName(String dataSeriesAbbreviation)
Return the DataSeries associated with the two-character canonical nameString
getCanonicalName()
Integer
getExternalBlockContentId()
DataSeriesType
getType()
static DataSeries
valueOf(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.
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Enum Constant Detail
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BF_BitFlags
public static final DataSeries BF_BitFlags
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CF_CompressionBitFlags
public static final DataSeries CF_CompressionBitFlags
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RI_RefId
public static final DataSeries RI_RefId
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RL_ReadLength
public static final DataSeries RL_ReadLength
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AP_AlignmentPositionOffset
public static final DataSeries AP_AlignmentPositionOffset
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RG_ReadGroup
public static final DataSeries RG_ReadGroup
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RN_ReadName
public static final DataSeries RN_ReadName
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NF_RecordsToNextFragment
public static final DataSeries NF_RecordsToNextFragment
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MF_MateBitFlags
public static final DataSeries MF_MateBitFlags
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NS_NextFragmentReferenceSequenceID
public static final DataSeries NS_NextFragmentReferenceSequenceID
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NP_NextFragmentAlignmentStart
public static final DataSeries NP_NextFragmentAlignmentStart
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TS_InsertSize
public static final DataSeries TS_InsertSize
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TL_TagIdList
public static final DataSeries TL_TagIdList
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TC_TagCount
public static final DataSeries TC_TagCount
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TN_TagNameAndType
public static final DataSeries TN_TagNameAndType
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MQ_MappingQualityScore
public static final DataSeries MQ_MappingQualityScore
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FN_NumberOfReadFeatures
public static final DataSeries FN_NumberOfReadFeatures
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FP_FeaturePosition
public static final DataSeries FP_FeaturePosition
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FC_FeatureCode
public static final DataSeries FC_FeatureCode
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BB_bases
public static final DataSeries BB_bases
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QQ_scores
public static final DataSeries QQ_scores
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BA_Base
public static final DataSeries BA_Base
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QS_QualityScore
public static final DataSeries QS_QualityScore
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BS_BaseSubstitutionCode
public static final DataSeries BS_BaseSubstitutionCode
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IN_Insertion
public static final DataSeries IN_Insertion
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DL_DeletionLength
public static final DataSeries DL_DeletionLength
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RS_RefSkip
public static final DataSeries RS_RefSkip
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SC_SoftClip
public static final DataSeries SC_SoftClip
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PD_padding
public static final DataSeries PD_padding
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HC_HardClip
public static final DataSeries HC_HardClip
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TM_TestMark
public static final DataSeries TM_TestMark
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TV_TestMark
public static final DataSeries TV_TestMark
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Method Detail
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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
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valueOf
public static DataSeries 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
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getType
public DataSeriesType getType()
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getCanonicalName
public String getCanonicalName()
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getExternalBlockContentId
public Integer getExternalBlockContentId()
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byCanonicalName
public static DataSeries byCanonicalName(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
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