cgatools::variants::CallDiffResult Struct Reference

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

#include <CallDiffResult.hpp>

List of all members.

Public Types
enum	MatchType {   REF_IDENTICAL = 0, ALT_IDENTICAL = 1, REF_CONSISTENT = 2, ALT_CONSISTENT = 3,   ONLY_A = 4, ONLY_B = 5, MISMATCH = 6, PHASE_MISMATCH = 7,   PLOIDY_MISMATCH = 8, MATCH_TYPE_LAST = 9 }
	Enumeration describing the type of match found one one allele. More...
Static Public Member Functions
static MatchType	mergeMatchTypes (MatchType mtA, 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 (MatchType mt)
	Returns string identifier associated with the given match type.
static std::string	getMatchTypeString (const std::vector< MatchType > &mt)
	Returns ;-separated string identifier for the given list of MatchType instances.
static std::string	getSimpleMatchTypeString (const std::vector< MatchType > &mt)
	Returns string identifier that is the simplified version of the match type identifier (i.e.
Public Attributes
size_t	lhsOffset_
	The offset in the list PhasedHypothesis of file A of the allele used for this CallDiffResult.
size_t	rhsOffset_
	The offset in the list PhasedHypothesis of file B of the allele used for this CallDiffResult.
std::vector< MatchType >	matchType_
	For each allele, the match type.
boost::array< std::vector < std::vector< std::pair < MatchType, const Call * > > >, 2 >	callClass_
	For each file, for each allele, for each call, the MatchType and Call.
std::vector< size_t >	perm_
	The permutation of file A used for this CallDiffResult.

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Detailed Description

Class to hold the result of diffing two superloci.

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Member Enumeration Documentation

enum cgatools::variants::CallDiffResult::MatchType

Enumeration describing the type of match found one one allele.

Enumerator:

REF_IDENTICAL	files identical, ref-consistent
ALT_IDENTICAL	files identical, ref-inconsistent
REF_CONSISTENT	files consistent, ref-consistent
ALT_CONSISTENT	files consistent, ref-inconsistent
ONLY_A	files inconsistent, A is ref-inconsistent
ONLY_B	files inconsistent, B is ref-inconsistent
MISMATCH	files inconsistent, both ref-inconsistent
PHASE_MISMATCH	files inconsistent, consistent if no hapLink
PLOIDY_MISMATCH	superlocus inconsistent ploidy

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Member Function Documentation

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

(

const std::vector< MatchType > &

mt

)

[static]

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

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

(

const std::vector< 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 MatchType cgatools::variants::CallDiffResult::mergeMatchTypes	(	MatchType	mtA,
		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<MatchType, const Call*> > >, 2> cgatools::variants::CallDiffResult::callClass_

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

size_t cgatools::variants::CallDiffResult::lhsOffset_

The offset in the list PhasedHypothesis of file A of the allele used for this CallDiffResult.

size_t cgatools::variants::CallDiffResult::rhsOffset_

The offset in the list PhasedHypothesis of file B of the allele used for this CallDiffResult.

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

• CallDiffResult.hpp