org.broadinstitute.hellbender.exceptions

Class UserException.MalformedFile

java.lang.Object

java.lang.Throwable

java.lang.Exception

java.lang.RuntimeException

org.broadinstitute.hellbender.exceptions.UserException

org.broadinstitute.hellbender.exceptions.UserException.MalformedFile

All Implemented Interfaces:

java.io.Serializable

Enclosing class:

UserException

public static class UserException.MalformedFile
extends UserException

Class UserException.MalformedFile

For errors parsing files

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.VQSRNegativeModelFailure, UserException.VQSRPositiveModelFailure, UserException.WrongFeatureType

Field Summary

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

MISSING_REFERENCE_FOR_CRAM

Constructor Summary

Constructors

Constructor and Description
MalformedFile(java.io.File f, java.lang.String message)
MalformedFile(java.io.File f, java.lang.String message, java.lang.Exception e)
MalformedFile(java.nio.file.Path p, java.lang.String message)
MalformedFile(java.nio.file.Path p, java.lang.String message, java.lang.Exception e)
MalformedFile(java.lang.String message)

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

MalformedFile

public MalformedFile(java.lang.String message)

MalformedFile

public MalformedFile(java.io.File f,
                     java.lang.String message)

MalformedFile

public MalformedFile(java.io.File f,
                     java.lang.String message,
                     java.lang.Exception e)

MalformedFile

public MalformedFile(java.nio.file.Path p,
                     java.lang.String message)

MalformedFile

public MalformedFile(java.nio.file.Path p,
                     java.lang.String message,
                     java.lang.Exception e)