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
struct	AlternativeCall
class	AlternativeCallsField
class	TotalScoreField
class	VarFilterField
class	VarQualityField
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.
void	addVarFilter (const std::string &filter)
	Adds a filter string to varFilter_ vector.
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 void	parseAlternativeCalls (const char *first, const char *last, std::vector< AlternativeCall > &alternativeCalls)
	Parse alternativeCalls field.
static void	parseVarFilter (const char *first, const char *last, std::vector< std::string > &varFilter)
	Parse varFilter field.
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.
std::vector< std::string >	varFilter_
	The varFilter 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.
std::string	alleleFreq_
	The alleleFreq column in the variant file.
std::vector< AlternativeCall >	alternativeCalls_
	The alternativeCalls 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.

---

Detailed Description

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

---

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.

---

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 "?".

std::vector<std::string> cgatools::variants::Call::varFilter_

The varFilter column in the variant file.

For old var files that have no varFilter or varQuality, this field is empty. For old var files with varQuality instead of varFilter, this field may be empty, VQLOW or PASS.

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.

---

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

• Call.hpp