Package picard.arrays.illumina
Enum Class Build37ExtendedIlluminaManifestRecord.Flag
java.lang.Object
java.lang.Enum<Build37ExtendedIlluminaManifestRecord.Flag>
picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
- All Implemented Interfaces:
Serializable
,Comparable<Build37ExtendedIlluminaManifestRecord.Flag>
,Constable
- Enclosing class:
- Build37ExtendedIlluminaManifestRecord
protected static enum Build37ExtendedIlluminaManifestRecord.Flag
extends Enum<Build37ExtendedIlluminaManifestRecord.Flag>
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum ConstantsEnum ConstantDescriptionThe record passes validation but is a duplicate (another assay at the same locus with the same alleles)Flagged by Illumina as a bad assayBoth insertion and deletion sequence found in reference.Deprecated.- but used in existing extended manifest files.Neither insertion nor deletion sequence found in reference.Deprecated.- but used in existing extended manifest files.Manifest contained no allele B probe sequenceThe record in the manifest passes validation and will be used in VCF generationProbe sequence not found in reference.Deprecated.- but used in existing extended manifest files.Deprecated.- but used in existing extended manifest files.Source sequence is invalid (contains invalid character).Deprecated.- but used in existing extended manifest files.Deprecated.- but used in existing extended manifest files. -
Method Summary
Modifier and TypeMethodDescriptionReturns the enum constant of this class with the specified name.values()
Returns an array containing the constants of this enum class, in the order they are declared.
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Enum Constant Details
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PASS
The record in the manifest passes validation and will be used in VCF generation -
DUPE
The record passes validation but is a duplicate (another assay at the same locus with the same alleles) -
ILLUMINA_FLAGGED
Flagged by Illumina as a bad assay -
LIFTOVER_FAILED
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UNSUPPORTED_GENOME_BUILD
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PROBE_SEQUENCE_MISMATCH
Probe sequence not found in reference. -
MISSING_ALLELE_B_PROBESEQ
Manifest contained no allele B probe sequence -
SOURCE_SEQUENCE_INVALID
Source sequence is invalid (contains invalid character). -
INDEL_NOT_FOUND
Neither insertion nor deletion sequence found in reference. -
INDEL_CONFLICT
Both insertion and deletion sequence found in reference. -
PROBE_SEQUENCE_STRAND_INVALID
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag PROBE_SEQUENCE_STRAND_INVALIDDeprecated.- but used in existing extended manifest files. -
SOURCE_SEQUENCE_MISMATCH
Deprecated.- but used in existing extended manifest files. -
SOURCE_SEQUENCE_STRAND_INVALID
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag SOURCE_SEQUENCE_STRAND_INVALIDDeprecated.- but used in existing extended manifest files. -
SEQUENCE_MISMATCH
Deprecated.- but used in existing extended manifest files. -
INDEL_SEQ_MISMATCH
Deprecated.- but used in existing extended manifest files. -
INDEL_EXTENSION_ERROR
Deprecated.- but used in existing extended manifest files.
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Method Details
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values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
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valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class has no constant with the specified nameNullPointerException
- if the argument is null
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