cgatools::variants::Call Struct Reference

A struct that corresponds to a single line of a Complete Genomics variant file. More...

#include <Call.hpp>

List of all members.

Classes
class	TotalScoreField
class	VarQualityField
Public Types
enum	VarQuality { VAR_QUALITY_EMPTY = 0, VAR_QUALITY_LOW = 1, VAR_QUALITY_HIGH = 2 }
Public Member Functions
	Call ()
	Construct an empty call.
std::string	calledSequence (const reference::CrrFile &crr) const
	Returns the called sequence as a string, replacing "=" with the corresponding reference sequence.
std::string	refSequence (const reference::CrrFile &crr) const
	Returns the reference sequence as a string, replacing "=" with the corresponding reference sequence.
bool	isRefConsistent (const reference::CrrFile &crr) const
	Returns true iff the alleleSeq_ is consistent with the reference.
bool	hasNoCalls () const
	Returns true iff this call's sequence sequence contains N or ? characters.
void	addFieldParsers (util::DelimitedFile &df, const reference::CrrFile &crr)
	Add fields to parser so that it can parse lines, putting data in this call.
std::ostream &	write (std::ostream &out, const reference::CrrFile &crr, const char sep= '\t') const
	Writes the call out, using the given separator charactor.
Static Public Member Functions
static const char *	varQualityToString (const VarQuality varQuality)
	Get the string form of varQuality.
static VarQuality	parseVarQuality (const char *first, const char *last)
	Parse a varQuality string.
static std::string	getHeader (const char separator= '\t')
	Returns header for a call output.
Public Attributes
uint32_t	locus_
	The locus column in the variant file.
uint16_t	ploidy_
	The ploidy column in the variant file.
uint16_t	haplotype_
	The haplotype column in the variant file.
reference::Range	range_
	The chromosome, begin, and end columns in the variant file.
std::string	varType_
	The varType column in the variant file.
std::string	reference_
	The reference column in the variant file.
std::string	alleleSeq_
	The alleleSeq column in the variant file.
int32_t	varScoreVAF_
	The varScoreVAF column in the variant file.
int32_t	varScoreEAF_
	The varScoreEAF column in the variant file.
VarQuality	varQuality_
	The varQuality column in the variant file.
std::string	hapLink_
	The hapLink column in the variant file.
std::string	xRef_
	The xRef column in the variant file.
Static Public Attributes
static const uint16_t	ALL_HAPLOTYPES
	The "all" haplotype == [1..ploidy_] haplotypes.
static const uint16_t	UNKNOWN_PLOIDY
	Unknown ploidy, normally in no-ref regions on genome.
static const int32_t	EMPTY_SCORE
	The in-memory score corresponding to empty score on disk.

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Detailed Description

A struct that corresponds to a single line of a Complete Genomics variant file.

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Member Function Documentation

void cgatools::variants::Call::addFieldParsers	(	util::DelimitedFile &	df,
		const reference::CrrFile &	crr
	)

Add fields to parser so that it can parse lines, putting data in this call.

std::string cgatools::variants::Call::calledSequence

(

const reference::CrrFile &

crr

)

const

Returns the called sequence as a string, replacing "=" with the corresponding reference sequence.

bool cgatools::variants::Call::hasNoCalls

(

)

const

Returns true iff this call's sequence sequence contains N or ? characters.

bool cgatools::variants::Call::isRefConsistent

(

const reference::CrrFile &

crr

)

const

Returns true iff the alleleSeq_ is consistent with the reference.

std::string cgatools::variants::Call::refSequence

(

const reference::CrrFile &

crr

)

const

Returns the reference sequence as a string, replacing "=" with the corresponding reference sequence.

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Member Data Documentation

uint16_t cgatools::variants::Call::haplotype_

The haplotype column in the variant file.

The value is Call::ALL_HAPLOTYPES if the variant file specifies "all".

uint16_t cgatools::variants::Call::ploidy_

The ploidy column in the variant file.

The value is Call::UNKNOWN_PLOIDY if the variant file specifies "?".

VarQuality cgatools::variants::Call::varQuality_

The varQuality column in the variant file.

For old var files that have no varQuality, this field gets VAR_QUALITY_EMPTY.

int32_t cgatools::variants::Call::varScoreEAF_

The varScoreEAF column in the variant file.

For older var files that have totalScore instead of varScoreVAF and varScoreEAF, the totalScore is filled into the varScoreEAF column.

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The documentation for this struct was generated from the following file:

• Call.hpp