org.broadinstitute.hellbender.exceptions

Class UserException.CouldNotReadInputFile

java.lang.Object

java.lang.Throwable

java.lang.Exception

java.lang.RuntimeException

org.broadinstitute.hellbender.exceptions.UserException

org.broadinstitute.hellbender.exceptions.UserException.CouldNotReadInputFile

All Implemented Interfaces:

java.io.Serializable

Enclosing class:

UserException

public static class UserException.CouldNotReadInputFile
extends UserException

Class UserException.CouldNotReadInputFile

For generic errors opening/reading from input 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
CouldNotReadInputFile(java.io.File file)
CouldNotReadInputFile(java.io.File file, java.lang.Exception e)
CouldNotReadInputFile(java.io.File file, java.lang.String message)
CouldNotReadInputFile(java.io.File file, java.lang.String message, java.lang.Exception e)
CouldNotReadInputFile(java.nio.file.Path file)
CouldNotReadInputFile(java.nio.file.Path path, java.lang.Exception e)
CouldNotReadInputFile(java.nio.file.Path file, java.lang.String message)
CouldNotReadInputFile(java.nio.file.Path file, java.lang.String message, java.lang.Throwable cause)
CouldNotReadInputFile(java.lang.String message)
CouldNotReadInputFile(java.lang.String message, java.lang.Exception e)
CouldNotReadInputFile(java.lang.String file, 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

CouldNotReadInputFile

public CouldNotReadInputFile(java.lang.String message,
                             java.lang.Exception e)

CouldNotReadInputFile

public CouldNotReadInputFile(java.io.File file)

CouldNotReadInputFile

public CouldNotReadInputFile(java.nio.file.Path file)

CouldNotReadInputFile

public CouldNotReadInputFile(java.io.File file,
                             java.lang.String message)

CouldNotReadInputFile

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

CouldNotReadInputFile

public CouldNotReadInputFile(java.nio.file.Path file,
                             java.lang.String message,
                             java.lang.Throwable cause)

CouldNotReadInputFile

public CouldNotReadInputFile(java.lang.String file,
                             java.lang.String message)

CouldNotReadInputFile

public CouldNotReadInputFile(java.io.File file,
                             java.lang.String message,
                             java.lang.Exception e)

CouldNotReadInputFile

public CouldNotReadInputFile(java.io.File file,
                             java.lang.Exception e)

CouldNotReadInputFile

public CouldNotReadInputFile(java.nio.file.Path path,
                             java.lang.Exception e)

CouldNotReadInputFile

public CouldNotReadInputFile(java.lang.String message)