SamValidationError Class Reference

The SamValidationError class describes a validation error that occured, containing the error type, severity, and textual error message. More...

#include <SamValidation.h>

Public Types
enum	Severity { WARNING , ERROR }
	Severity of the error. More...
enum	Type {   INVALID_QNAME , INVALID_REF_ID , INVALID_RNAME , INVALID_POS ,   INVALID_MAPQ , INVALID_CIGAR , INVALID_MRNM , INVALID_QUAL ,   INVALID_TAG }
	Type of the error. More...

Public Member Functions
	SamValidationError (Type type, Severity severity, std::string Message)
	Constructor that sets the type, severity, and message for the validation error.
Type	getType () const
	Return the type enum of this validation error object.
Severity	getSeverity () const
	Return the severity enum of this validation error object.
const char *	getMessage () const
	Return the error message of this validation error object.
const char *	getTypeString () const
	Return the string representing this object's type of validation error.
const char *	getSeverityString () const
	Return the string representing this object's severity of validation error.
void	getErrorString (std::string &errorString) const
	Get the error string representing this object's error.
void	printError () const
	Print a formatted output of the error to cerr.

Static Public Member Functions
static const char *	getTypeString (Type type)
	Get the string representing the specified type of validation error.

Detailed Description

The SamValidationError class describes a validation error that occured, containing the error type, severity, and textual error message.

Definition at line 34 of file SamValidation.h.

Member Enumeration Documentation

Severity

enum SamValidationError::Severity

Severity of the error.

Enumerator
WARNING	Warning is used if it is just an invalid value.
ERROR	Error is used if parsing could not succeed.

Definition at line 38 of file SamValidation.h.

        {
            WARNING, ///< Warning is used if it is just an invalid value.
            ERROR    ///< Error is used if parsing could not succeed.
        };

Type

enum SamValidationError::Type

Type of the error.

TODO: NOT ALL INVALID TYPES HAVE BEEN ADDED SINCE NOT ALL VALIDATION IS COMPLETE YET

Enumerator
INVALID_QNAME	Invalid read/query name.
INVALID_REF_ID	Invalid reference id.
INVALID_RNAME	Invalid reference name.
INVALID_POS	Invalid position.
INVALID_MAPQ	Invalid mapping quality.
INVALID_CIGAR	Invalid CIGAR.
INVALID_MRNM	Invalid mate/next fragment reference name.
INVALID_QUAL	Invalid base quality.
INVALID_TAG	Invalid tag.

Definition at line 47 of file SamValidation.h.

        {
            INVALID_QNAME, ///< Invalid read/query name
            INVALID_REF_ID, ///< Invalid reference id
            INVALID_RNAME, ///< Invalid reference name
            INVALID_POS, ///< Invalid position
            INVALID_MAPQ, ///< Invalid mapping quality
            INVALID_CIGAR, ///< Invalid CIGAR
            INVALID_MRNM, ///< Invalid mate/next fragment reference name
            INVALID_QUAL, ///< Invalid base quality
            INVALID_TAG ///< Invalid tag
        };

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The documentation for this class was generated from the following files:

• bam/SamValidation.h
• bam/SamValidation.cpp