sv_types Namespace Reference

Typedefs
using	SVEvidenceFlags = std::bitset< 10 >

Enumerations
enum class	SVType {   UNKNOWN = -1 , DEL = 0 , DUP = 1 , INV = 2 ,   INS = 3 , BND = 4 , NEUTRAL = 5 , LOH = 6 }
enum class	Genotype { HOMOZYGOUS_REF = 0 , HETEROZYGOUS = 1 , HOMOZYGOUS_ALT = 2 , UNKNOWN = 3 }
enum class	SVDataType {   CIGARINS = 0 , CIGARDEL = 1 , CIGARCLIP = 2 , SPLIT = 3 ,   SPLITDIST1 = 4 , SPLITDIST2 = 5 , SPLITINV = 6 , SUPPINV = 7 ,   HMM = 8 , UNKNOWN = 9 }

Functions
std::string	getSVTypeString (SVType sv_type)
std::string	getSVAlignmentTypeString (SVEvidenceFlags aln_type)
SVType	getSVTypeFromCNState (int cn_state)
std::string	getGenotypeString (Genotype genotype)
std::string	getSVTypeSymbol (SVType sv_type)
bool	isValidCopyNumberUpdate (SVType sv_type, SVType updated_sv_type)

Variables
const std::unordered_map< SVType, std::string >	SVTypeString
const std::unordered_map< SVType, std::string >	SVTypeSymbol
const std::unordered_map< Genotype, std::string >	GenotypeString
const std::unordered_map< SVDataType, std::string >	SVDataTypeString
const std::unordered_map< int, SVType >	CNVTypeMap

Typedef Documentation

SVEvidenceFlags

using sv_types::SVEvidenceFlags = typedef std::bitset<10>

Enumeration Type Documentation

Genotype

enum class sv_types::Genotype

strong

Enumerator
HOMOZYGOUS_REF
HETEROZYGOUS
HOMOZYGOUS_ALT
UNKNOWN

SVDataType

enum class sv_types::SVDataType

strong

Enumerator
CIGARINS
CIGARDEL
CIGARCLIP
SPLIT
SPLITDIST1
SPLITDIST2
SPLITINV
SUPPINV
HMM
UNKNOWN

SVType

enum class sv_types::SVType

strong

Enumerator
UNKNOWN
DEL
DUP
INV
INS
BND
NEUTRAL
LOH

Function Documentation

getGenotypeString()

std::string sv_types::getGenotypeString ( Genotype  genotype )

inline

getSVAlignmentTypeString()

std::string sv_types::getSVAlignmentTypeString ( SVEvidenceFlags  aln_type )

inline

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getSVTypeFromCNState()

SVType sv_types::getSVTypeFromCNState ( int  cn_state )

inline

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getSVTypeString()

std::string sv_types::getSVTypeString ( SVType  sv_type )

inline

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getSVTypeSymbol()

std::string sv_types::getSVTypeSymbol ( SVType  sv_type )

inline

isValidCopyNumberUpdate()

bool sv_types::isValidCopyNumberUpdate ( SVType  sv_type, SVType  updated_sv_type  )

inline

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Variable Documentation

CNVTypeMap

const std::unordered_map<int, SVType> sv_types::CNVTypeMap

Initial value:

= {
        {0, SVType::UNKNOWN},
        {1, SVType::DEL},
        {2, SVType::DEL},
        {3, SVType::NEUTRAL},
        {4, SVType::LOH},
        {5, SVType::DUP},
        {6, SVType::DUP}
    }

GenotypeString

const std::unordered_map<Genotype, std::string> sv_types::GenotypeString

Initial value:

= {
        {Genotype::HOMOZYGOUS_REF, "0/0"},
        {Genotype::HETEROZYGOUS, "0/1"},
        {Genotype::HOMOZYGOUS_ALT, "1/1"},
        {Genotype::UNKNOWN, "./."}
    }

SVDataTypeString

const std::unordered_map<SVDataType, std::string> sv_types::SVDataTypeString

Initial value:

= {
        {SVDataType::CIGARINS, "CIGARINS"},
        {SVDataType::CIGARDEL, "CIGARDEL"},
        {SVDataType::CIGARCLIP, "CIGARCLIP"},
        {SVDataType::SPLIT, "SPLIT"},
        {SVDataType::SPLITDIST1, "SPLITDIST1"},
        {SVDataType::SPLITDIST2, "SPLITDIST2"},
        {SVDataType::SPLITINV, "SPLITINV"},
        {SVDataType::SUPPINV, "SUPPINV"},
        {SVDataType::HMM, "HMM"},
        {SVDataType::UNKNOWN, "UNKNOWN"}
    }

SVTypeString

const std::unordered_map<SVType, std::string> sv_types::SVTypeString

Initial value:

= {
        {SVType::UNKNOWN, "UNKNOWN"},
        {SVType::DEL, "DEL"},
        {SVType::DUP, "DUP"},
        {SVType::INV, "INV"},
        {SVType::INS, "INS"},
        {SVType::BND, "BND"},
        {SVType::NEUTRAL, "NEUTRAL"},
        {SVType::LOH, "LOH"}
    }

SVTypeSymbol

const std::unordered_map<SVType, std::string> sv_types::SVTypeSymbol

Initial value:

= {
        {SVType::UNKNOWN, "."},
        {SVType::DEL, "<DEL>"},
        {SVType::DUP, "<DUP>"},
        {SVType::INV, "<INV>"},
        {SVType::INS, "<INS>"},
        {SVType::BND, "<BND>"},
    }