Safe Haskell	None
Language	Haskell2010

Bio.VCF.Internal.Types

Contents

Orphan instances

Documentation

data VCF Source #

Constructors

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

Instances

Eq VCF Source #
Methods (==) :: VCF -> VCF -> Bool # (/=) :: VCF -> VCF -> Bool #
Show VCF Source #
Methods showsPrec :: Int -> VCF -> ShowS # show :: VCF -> String # showList :: [VCF] -> ShowS #
Generic VCF Source #
Associated Types type Rep VCF :: * -> * # Methods from :: VCF -> Rep VCF x # to :: Rep VCF x -> VCF #
ToJSON VCF Source #
Methods toJSON :: VCF -> Value # toEncoding :: VCF -> Encoding # toJSONList :: [VCF] -> Value # toEncodingList :: [VCF] -> Encoding #
FromJSON VCF Source #
Methods parseJSON :: Value -> Parser VCF # parseJSONList :: Value -> Parser [VCF] #
type Rep VCF Source #
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 Source #

Constructors

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

data Variation Source #

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 Source #
Methods (==) :: Variation -> Variation -> Bool # (/=) :: Variation -> Variation -> Bool #
Show Variation Source #
Methods showsPrec :: Int -> Variation -> ShowS # show :: Variation -> String # showList :: [Variation] -> ShowS #
Generic Variation Source #
Associated Types type Rep Variation :: * -> * # Methods from :: Variation -> Rep Variation x # to :: Rep Variation x -> Variation #
ToJSON Variation Source #
Methods toJSON :: Variation -> Value # toEncoding :: Variation -> Encoding # toJSONList :: [Variation] -> Value # toEncodingList :: [Variation] -> Encoding #
FromJSON Variation Source #
Methods parseJSON :: Value -> Parser Variation # parseJSONList :: Value -> Parser [Variation] #
type Rep Variation Source #
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] Source #

newtype Patient Source #

Constructors

Patient ByteString

Instances

Eq Patient Source #
Methods (==) :: Patient -> Patient -> Bool # (/=) :: Patient -> Patient -> Bool #
Show Patient Source #
Methods showsPrec :: Int -> Patient -> ShowS # show :: Patient -> String # showList :: [Patient] -> ShowS #
Generic Patient Source #
Associated Types type Rep Patient :: * -> * # Methods from :: Patient -> Rep Patient x # to :: Rep Patient x -> Patient #
ToJSON Patient Source #
Methods toJSON :: Patient -> Value # toEncoding :: Patient -> Encoding # toJSONList :: [Patient] -> Value # toEncodingList :: [Patient] -> Encoding #
FromJSON Patient Source #
Methods parseJSON :: Value -> Parser Patient # parseJSONList :: Value -> Parser [Patient] #
type Rep Patient Source #
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 Source #
Methods toJSON :: ByteString -> Value # toEncoding :: ByteString -> Encoding # toJSONList :: [ByteString] -> Value # toEncodingList :: [ByteString] -> Encoding #
FromJSON ByteString Source #
Methods parseJSON :: Value -> Parser ByteString # parseJSONList :: Value -> Parser [ByteString] #

Eq Header Source #
Methods (==) :: Header -> Header -> Bool # (/=) :: Header -> Header -> Bool #
Show Header Source #
Methods showsPrec :: Int -> Header -> ShowS # show :: Header -> String # showList :: [Header] -> ShowS #
Generic Header Source #
Associated Types type Rep Header :: * -> * # Methods from :: Header -> Rep Header x # to :: Rep Header x -> Header #
ToJSON Header Source #
Methods toJSON :: Header -> Value # toEncoding :: Header -> Encoding # toJSONList :: [Header] -> Value # toEncodingList :: [Header] -> Encoding #
FromJSON Header Source #
Methods parseJSON :: Value -> Parser Header # parseJSONList :: Value -> Parser [Header] #
type Rep Header Source #
type Rep Header