cgatools::variants::CallDiffResult Class Reference

Class to hold the result of diffing two superloci. More...

#include <CallDiffResult.hpp>

List of all members.

Public Member Functions
void	setHypotheses (const PhasedHypothesis &lhs, const PhasedHypothesis &rhs, const std::vector< size_t > &perm)
Static Public Member Functions
static cdmt::MatchType	mergeMatchTypes (cdmt::MatchType mtA, cdmt::MatchType mtB)
	For calls participating in two CallDiffSegment instances or alleles having multiple calls, this returns the merged match type associated with the call or allele as a whole.
static const char *	getMatchTypeString (cdmt::MatchType mt)
	Returns string identifier associated with the given match type.
static std::string	getMatchTypeString (const std::vector< cdmt::MatchType > &mt)
	Returns ;-separated string identifier for the given list of cdmt::MatchType instances.
static std::string	getSimpleMatchTypeString (const std::vector< cdmt::MatchType > &mt)
	Returns string identifier that is the simplified version of the match type identifier (i.e.
static bool	isConsistent (cdmt::MatchType mt)
	Returns true for the identical and compatible match types.
static bool	isIdentical (cdmt::MatchType mt)
	Returns true for the identical match types.
Public Attributes
std::vector< cdmt::MatchType >	matchType_
	For each allele, the match type.
std::vector< cdmt::MatchType >	matchTypeBySegment_
	For each allele, the match type if the broken-down AlleleDiffSegments are used.
boost::array< PhasedHypothesis, 2 >	hyp_
	For each file, the PhasedHypothesis for this CallDiffResult.
boost::array< std::vector < std::vector< std::pair < cdmt::MatchType, const Call * > > >, 2 >	callClass_
	For each file, for each allele, for each call, the cdmt::MatchType and Call.

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Detailed Description

Class to hold the result of diffing two superloci.

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Member Function Documentation

static std::string cgatools::variants::CallDiffResult::getMatchTypeString

(

const std::vector< cdmt::MatchType > &

mt

)

[static]

Returns ;-separated string identifier for the given list of cdmt::MatchType instances.

static std::string cgatools::variants::CallDiffResult::getSimpleMatchTypeString

(

const std::vector< cdmt::MatchType > &

mt

)

[static]

Returns string identifier that is the simplified version of the match type identifier (i.e.

ref-identical -> identical, alt-identical -> identical).

static cdmt::MatchType cgatools::variants::CallDiffResult::mergeMatchTypes	(	cdmt::MatchType	mtA,
		cdmt::MatchType	mtB
	)			[static]

For calls participating in two CallDiffSegment instances or alleles having multiple calls, this returns the merged match type associated with the call or allele as a whole.

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Member Data Documentation

boost::array<std::vector< std::vector< std::pair<cdmt::MatchType, const Call*> > >, 2> cgatools::variants::CallDiffResult::callClass_

For each file, for each allele, for each call, the cdmt::MatchType and Call.

std::vector<cdmt::MatchType> cgatools::variants::CallDiffResult::matchTypeBySegment_

For each allele, the match type if the broken-down AlleleDiffSegments are used.

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

• CallDiffResult.hpp