SamValidator Class Reference

List of all members.

Static Public Member Functions
static bool	isValid (SamFileHeader &samHeader, SamRecord &samRecord, SamValidationErrors &validationErrors)
static bool	isValidQname (const char *qname, uint8_t qnameLen, SamValidationErrors &validationErrors)
static bool	isValidFlag (uint16_t flag, SamValidationErrors &validationErrors)
static bool	isValidRname (SamFileHeader &samHeader, const char *rname, SamValidationErrors &validationErrors)
static bool	isValidRname (const char *rname, SamValidationErrors &validationErrors)
static bool	isValidRefID (int32_t refID, const SamReferenceInfo &refInfo, SamValidationErrors &validationErrors)
static bool	isValid1BasedPos (int32_t pos, SamValidationErrors &validationErrors)
static bool	isValidMapQuality (uint8_t mapQuality, SamValidationErrors &validationErrors)
static bool	isValidSequence (SamRecord &samRecord, SamValidationErrors &validationErrors)
	Validate the sequence, but not against the cigar or quality string.
static bool	isValidCigar (SamRecord &samRecord, SamValidationErrors &validationErrors)
	Cigar validation depends on sequence.
static bool	isValidCigar (const char *cigar, const char *sequence, SamValidationErrors &validationErrors)
static bool	isValidCigar (const char *cigar, int seqLen, SamValidationErrors &validationErrors)
static bool	isValidMrnm ()
static bool	isValidMpos ()
static bool	isValidIsize ()
static bool	isValidSeq ()
static bool	isValidQuality (SamRecord &samRecord, SamValidationErrors &validationErrors)
static bool	isValidQuality (const char *quality, const char *sequence, SamValidationErrors &validationErrors)
static bool	isValidQuality (const char *quality, int seqLength, SamValidationErrors &validationErrors)
static bool	isValidTags (SamRecord &samRecord, SamValidationErrors &validationErrors)
static bool	isValidVtype ()
static bool	isValidValue ()

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Detailed Description

Definition at line 135 of file SamValidation.h.

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Member Function Documentation

bool SamValidator::isValidSequence	(	SamRecord &	samRecord,
		SamValidationErrors &	validationErrors
	)			[static]

Validate the sequence, but not against the cigar or quality string.

Validation against cigar is done in isValidCigar. Validation against the quality string is done in isValidQuality.

Definition at line 536 of file SamValidation.cpp.

{
    return(true);
}

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

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