Bio.VCF.Internal.Types

Documentation

data VCF

Constructors

VCF

Fields

• header :: !Header
• variations :: ![(Variation, [ByteString])]

Instances

Eq VCF

Methods

(==) :: VCF -> VCF -> Bool

(/=) :: VCF -> VCF -> Bool

Show VCF

Methods

showsPrec :: Int -> VCF -> ShowS

show :: VCF -> String

showList :: [VCF] -> ShowS

Generic VCF

Associated Types

type Rep VCF :: * -> *

Methods

from :: VCF -> Rep VCF x

to :: Rep VCF x -> VCF

ToJSON VCF

Methods

toJSON :: VCF -> Value

toEncoding :: VCF -> Encoding

toJSONList :: [VCF] -> Value

toEncodingList :: [VCF] -> Encoding

FromJSON VCF

Methods

parseJSON :: Value -> Parser VCF

parseJSONList :: Value -> Parser [VCF]

type Rep VCF

type Rep VCF = D1 (MetaData "VCF" "Bio.VCF.Internal.Types" "vcf-0.9.0-DOeTEQ1chbDHNrDu67LExk" False) (C1 (MetaCons "VCF" PrefixI True) ((:*:) (S1 (MetaSel (Just Symbol "header") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 Header)) (S1 (MetaSel (Just Symbol "variations") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 [(Variation, [ByteString])]))))

data Header

Constructors

Header

Fields

• fileFormat :: !ByteString
• informationFields :: ![InformationField]
• filterFields :: ![FilterField]
• formatFields :: ![FormatField]
• alternativeAlleleFields :: ![AlternativeAlleleField]
• assemblyField :: !ByteString
• contigFields :: ![ContigField]
• sampleFields :: ![SampleField]
• pedigreeFields :: !PedigreeInformation

Instances

Eq Header

Methods

(==) :: Header -> Header -> Bool

(/=) :: Header -> Header -> Bool

Show Header

Methods

showsPrec :: Int -> Header -> ShowS

show :: Header -> String

showList :: [Header] -> ShowS

Generic Header

Associated Types

type Rep Header :: * -> *

Methods

from :: Header -> Rep Header x

to :: Rep Header x -> Header

ToJSON Header

Methods

toJSON :: Header -> Value

toEncoding :: Header -> Encoding

toJSONList :: [Header] -> Value

toEncodingList :: [Header] -> Encoding

FromJSON Header

Methods

parseJSON :: Value -> Parser Header

parseJSONList :: Value -> Parser [Header]

type Rep Header

type Rep Header

data Variation

Constructors

Variation

Fields

• chrom :: !ByteString
• pos :: !Int
• idx :: ![ByteString]
• ref :: !ByteString
• alt :: ![ByteString]
• qual :: !(Maybe Float)
• filt :: ![ByteString]
• info :: ![ByteString]
• format :: !(Maybe [ByteString])

Instances

Eq Variation

Methods

(==) :: Variation -> Variation -> Bool

(/=) :: Variation -> Variation -> Bool

Show Variation

Methods

showsPrec :: Int -> Variation -> ShowS

show :: Variation -> String

showList :: [Variation] -> ShowS

Generic Variation

Associated Types

type Rep Variation :: * -> *

Methods

from :: Variation -> Rep Variation x

to :: Rep Variation x -> Variation

ToJSON Variation

Methods

toJSON :: Variation -> Value

toEncoding :: Variation -> Encoding

toJSONList :: [Variation] -> Value

toEncodingList :: [Variation] -> Encoding

FromJSON Variation

Methods

parseJSON :: Value -> Parser Variation

parseJSONList :: Value -> Parser [Variation]

type Rep Variation

type Rep Variation = D1 (MetaData "Variation" "Bio.VCF.Internal.Types" "vcf-0.9.0-DOeTEQ1chbDHNrDu67LExk" False) (C1 (MetaCons "Variation" PrefixI True) ((:*:) ((:*:) ((:*:) (S1 (MetaSel (Just Symbol "chrom") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 ByteString)) (S1 (MetaSel (Just Symbol "pos") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 Int))) ((:*:) (S1 (MetaSel (Just Symbol "idx") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 [ByteString])) (S1 (MetaSel (Just Symbol "ref") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 ByteString)))) ((:*:) ((:*:) (S1 (MetaSel (Just Symbol "alt") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 [ByteString])) (S1 (MetaSel (Just Symbol "qual") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Maybe Float)))) ((:*:) (S1 (MetaSel (Just Symbol "filt") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 [ByteString])) ((:*:) (S1 (MetaSel (Just Symbol "info") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 [ByteString])) (S1 (MetaSel (Just Symbol "format") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Maybe [ByteString]))))))))

type Genotypes = [ByteString]

newtype Patient

Constructors

Patient ByteString

Instances

Eq Patient

Methods

(==) :: Patient -> Patient -> Bool

(/=) :: Patient -> Patient -> Bool

Show Patient

Methods

showsPrec :: Int -> Patient -> ShowS

show :: Patient -> String

showList :: [Patient] -> ShowS

Generic Patient

Associated Types

type Rep Patient :: * -> *

Methods

from :: Patient -> Rep Patient x

to :: Rep Patient x -> Patient

ToJSON Patient

Methods

toJSON :: Patient -> Value

toEncoding :: Patient -> Encoding

toJSONList :: [Patient] -> Value

toEncodingList :: [Patient] -> Encoding

FromJSON Patient

Methods

parseJSON :: Value -> Parser Patient

parseJSONList :: Value -> Parser [Patient]

type Rep Patient

type Rep Patient = D1 (MetaData "Patient" "Bio.VCF.Internal.Types" "vcf-0.9.0-DOeTEQ1chbDHNrDu67LExk" True) (C1 (MetaCons "Patient" PrefixI False) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

Orphan instances

ToJSON ByteString

Methods

toJSON :: ByteString -> Value

toEncoding :: ByteString -> Encoding

toJSONList :: [ByteString] -> Value

toEncodingList :: [ByteString] -> Encoding

FromJSON ByteString

Methods

parseJSON :: Value -> Parser ByteString

parseJSONList :: Value -> Parser [ByteString]