| GATKException |
|
| GATKException.MissingReadField |
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| GATKException.ReadAttributeTypeMismatch |
|
| GATKException.ShouldNeverReachHereException |
For wrapping errors that are believed to never be reachable |
| PicardNonZeroExitException |
Exception used to propagate non-zero return values from Picard tools.
|
| UserException |
|
| UserException.BadInput |
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| UserException.BadTempDir |
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| UserException.CannotExecuteScript |
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| UserException.CannotHandleGzippedRef |
|
| UserException.CouldNotCreateOutputFile |
Class UserException.CouldNotCreateOutputFile
For generic errors writing to output files |
| UserException.CouldNotIndexFile |
|
| UserException.CouldNotReadInputFile |
Class UserException.CouldNotReadInputFile
For generic errors opening/reading from input files |
| UserException.EmptyIntersection |
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| UserException.FailsStrictValidation |
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| UserException.HardwareFeatureException |
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| UserException.HeaderMissingReadGroup |
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| UserException.IncompatibleRecalibrationTableParameters |
|
| UserException.IncompatibleSequenceDictionaries |
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| UserException.LexicographicallySortedSequenceDictionary |
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| UserException.MalformedBAM |
|
| UserException.MalformedFile |
Class UserException.MalformedFile
For errors parsing files |
| UserException.MalformedGenomeLoc |
|
| UserException.MalformedRead |
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| UserException.MisencodedQualityScoresRead |
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| UserException.MissingContigInSequenceDictionary |
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| UserException.MissingIndex |
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| UserException.MissingReference |
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| UserException.MissingReferenceDictFile |
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| UserException.MissingReferenceFaiFile |
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| UserException.MissingReferenceGziFile |
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| UserException.NoSuitableCodecs |
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| UserException.ReadMissingReadGroup |
|
| UserException.SequenceDictionaryIsMissingContigLengths |
|
| UserException.UnimplementedFeature |
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| UserException.VQSRNegativeModelFailure |
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| UserException.VQSRPositiveModelFailure |
|
| UserException.WrongFeatureType |
|