org.broadinstitute.hellbender.exceptions

Class UserException.LexicographicallySortedSequenceDictionary

java.lang.Object

java.lang.Throwable

java.lang.Exception

java.lang.RuntimeException

org.broadinstitute.hellbender.exceptions.UserException

org.broadinstitute.hellbender.exceptions.UserException.LexicographicallySortedSequenceDictionary

All Implemented Interfaces:

java.io.Serializable

Enclosing class:

UserException

public static class UserException.LexicographicallySortedSequenceDictionary
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.NoSuitableCodecs, UserException.ReadMissingReadGroup, UserException.Require2BitReferenceForBroadcast, UserException.UnimplementedFeature, UserException.WrongFeatureType

Constructor Summary

Constructors

Constructor and Description
LexicographicallySortedSequenceDictionary(java.lang.String name, 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 Detail

LexicographicallySortedSequenceDictionary

public LexicographicallySortedSequenceDictionary(java.lang.String name,
                                                 htsjdk.samtools.SAMSequenceDictionary dict)