Package org.broadinstitute.hellbender.exceptions

Class UserException.SequenceDictionaryIsMissingContigLengths

java.lang.Object

java.lang.Throwable

java.lang.Exception

java.lang.RuntimeException

org.broadinstitute.hellbender.exceptions.UserException

org.broadinstitute.hellbender.exceptions.UserException.SequenceDictionaryIsMissingContigLengths

All Implemented Interfaces:

Serializable

Enclosing class:

UserException

public static class UserException.SequenceDictionaryIsMissingContigLengths
extends UserException

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.exceptions.UserException

UserException.BadInput, UserException.BadTempDir, UserException.CannotExecuteScript, UserException.CannotHandleGzippedRef, UserException.CouldNotCreateOutputFile, UserException.CouldNotIndexFile, UserException.CouldNotReadInputFile, UserException.EmptyIntersection, UserException.FailsStrictValidation, UserException.HardwareFeatureException, UserException.HeaderMissingReadGroup, UserException.IncompatibleRecalibrationTableParameters, UserException.IncompatibleSequenceDictionaries, UserException.LexicographicallySortedSequenceDictionary, UserException.MalformedBAM, UserException.MalformedFile, UserException.MalformedGenomeLoc, UserException.MalformedRead, UserException.MisencodedQualityScoresRead, UserException.MissingContigInSequenceDictionary, UserException.MissingIndex, UserException.MissingReference, UserException.MissingReferenceDictFile, UserException.MissingReferenceFaiFile, UserException.MissingReferenceGziFile, UserException.NoSuitableCodecs, UserException.ReadMissingReadGroup, UserException.SequenceDictionaryIsMissingContigLengths, UserException.UnimplementedFeature, UserException.ValidationFailure, UserException.VQSRNegativeModelFailure, UserException.VQSRPositiveModelFailure, UserException.WarnableAnnotationFailure, UserException.WrongFeatureType

Field Summary

Fields inherited from class org.broadinstitute.hellbender.exceptions.UserException

MISSING_REFERENCE_FOR_CRAM

Constructor Summary

Constructors

Constructor	Description
SequenceDictionaryIsMissingContigLengths(String source, htsjdk.samtools.SAMSequenceDictionary dict)

Method Summary

Methods inherited from class org.broadinstitute.hellbender.exceptions.UserException

getMessage

Methods inherited from class java.lang.Throwable

addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString

Methods inherited from class java.lang.Object

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

Constructor Details

SequenceDictionaryIsMissingContigLengths

public SequenceDictionaryIsMissingContigLengths(String source,
 htsjdk.samtools.SAMSequenceDictionary dict)