Safe Haskell	Safe-Inferred
Language	Haskell2010

Poseidon.Janno

Synopsis

data JannoRow = JannoRow {
- jPoseidonID :: String
- jGeneticSex :: GeneticSex
- jGroupName :: ListColumn GroupName
- jAlternativeIDs :: Maybe (ListColumn JannoAlternativeID)
- jRelationTo :: Maybe (ListColumn JannoRelationTo)
- jRelationDegree :: Maybe (ListColumn JannoRelationDegree)
- jRelationType :: Maybe (ListColumn JannoRelationType)
- jRelationNote :: Maybe JannoRelationNote
- jCollectionID :: Maybe JannoCollectionID
- jCountry :: Maybe JannoCountry
- jCountryISO :: Maybe JannoCountryISO
- jLocation :: Maybe JannoLocation
- jSite :: Maybe JannoSite
- jLatitude :: Maybe JannoLatitude
- jLongitude :: Maybe JannoLongitude
- jDateType :: Maybe JannoDateType
- jDateC14Labnr :: Maybe (ListColumn JannoDateC14Labnr)
- jDateC14UncalBP :: Maybe (ListColumn JannoDateC14UncalBP)
- jDateC14UncalBPErr :: Maybe (ListColumn JannoDateC14UncalBPErr)
- jDateBCADStart :: Maybe JannoDateBCADStart
- jDateBCADMedian :: Maybe JannoDateBCADMedian
- jDateBCADStop :: Maybe JannoDateBCADStop
- jDateNote :: Maybe JannoDateNote
- jMTHaplogroup :: Maybe JannoMTHaplogroup
- jYHaplogroup :: Maybe JannoYHaplogroup
- jSourceTissue :: Maybe (ListColumn JannoSourceTissue)
- jNrLibraries :: Maybe JannoNrLibraries
- jLibraryNames :: Maybe (ListColumn JannoLibraryName)
- jCaptureType :: Maybe (ListColumn JannoCaptureType)
- jUDG :: Maybe JannoUDG
- jLibraryBuilt :: Maybe JannoLibraryBuilt
- jGenotypePloidy :: Maybe JannoGenotypePloidy
- jDataPreparationPipelineURL :: Maybe JannoDataPreparationPipelineURL
- jEndogenous :: Maybe JannoEndogenous
- jNrSNPs :: Maybe JannoNrSNPs
- jCoverageOnTargets :: Maybe JannoCoverageOnTargets
- jDamage :: Maybe JannoDamage
- jContamination :: Maybe (ListColumn JannoContamination)
- jContaminationErr :: Maybe (ListColumn JannoContaminationErr)
- jContaminationMeas :: Maybe (ListColumn JannoContaminationMeas)
- jContaminationNote :: Maybe JannoContaminationNote
- jGeneticSourceAccessionIDs :: Maybe (ListColumn JannoGeneticSourceAccessionID)
- jPrimaryContact :: Maybe JannoPrimaryContact
- jPublication :: Maybe (ListColumn JannoPublication)
- jComments :: Maybe JannoComment
- jKeywords :: Maybe (ListColumn JannoKeyword)
- jAdditionalColumns :: CsvNamedRecord
}
newtype GeneticSex = GeneticSex {
- sfSex :: Sex
}
newtype GroupName = GroupName Text
newtype ListColumn a = ListColumn {
- getListColumn :: [a]
}
data Sex
- = Male
- | Female
- | Unknown
newtype JannoCountryISO = JannoCountryISO Country
newtype JannoLatitude = JannoLatitude Double
newtype JannoLongitude = JannoLongitude Double
data JannoDateType
- = C14
- | Contextual
- | Modern
newtype JannoDateBCADMedian = JannoDateBCADMedian Int
data JannoCaptureType
- = Shotgun
- | A1240K
- | ArborComplete
- | ArborPrimePlus
- | ArborAncestralPlus
- | TwistAncientDNA
- | OtherCapture
- | ReferenceGenome
data JannoGenotypePloidy
- = Diploid
- | Haploid
data JannoUDG
- = Minus
- | Half
- | Plus
- | Mixed
data JannoRelationDegree
- = Identical
- | First
- | Second
- | ThirdToFifth
- | SixthToTenth
- | Unrelated
- | OtherDegree
data JannoLibraryBuilt
- = DS
- | SS
- | MixedSSDS
- | Other
writeJannoFile :: FilePath -> JannoRows -> IO ()
writeJannoFileWithoutEmptyCols :: FilePath -> JannoRows -> IO ()
readJannoFile :: FilePath -> PoseidonIO JannoRows
createMinimalJanno :: [EigenstratIndEntry] -> JannoRows
createMinimalSample :: EigenstratIndEntry -> JannoRow
jannoHeaderString :: [String]
newtype CsvNamedRecord = CsvNamedRecord NamedRecord
newtype JannoRows = JannoRows {
- getJannoRows :: [JannoRow]
}
type JannoStringList = ListColumn String
filterLookup :: FromField a => NamedRecord -> ByteString -> Parser a
filterLookupOptional :: FromField a => NamedRecord -> ByteString -> Parser (Maybe a)
getCsvNR :: CsvNamedRecord -> NamedRecord
encodingOptions :: EncodeOptions
decodingOptions :: DecodeOptions
explicitNA :: NamedRecord -> NamedRecord
removeUselessSuffix :: String -> String
parseCsvParseError :: Parser CsvParseError
renderCsvParseError :: CsvParseError -> String
getMaybeListColumn :: Maybe (ListColumn a) -> [a]
jannoRows2EigenstratIndEntries :: JannoRows -> [EigenstratIndEntry]
makeHeaderWithAdditionalColumns :: [JannoRow] -> Header

Documentation

data JannoRow Source #

A data type to represent a sample/janno file row See https://github.com/poseidon-framework/poseidon2-schema/blob/master/janno_columns.tsv for more details

Constructors

JannoRow

Fields

jPoseidonID :: String
jGeneticSex :: GeneticSex
jGroupName :: ListColumn GroupName
jAlternativeIDs :: Maybe (ListColumn JannoAlternativeID)
jRelationTo :: Maybe (ListColumn JannoRelationTo)
jRelationDegree :: Maybe (ListColumn JannoRelationDegree)
jRelationType :: Maybe (ListColumn JannoRelationType)
jRelationNote :: Maybe JannoRelationNote
jCollectionID :: Maybe JannoCollectionID
jCountry :: Maybe JannoCountry
jCountryISO :: Maybe JannoCountryISO
jLocation :: Maybe JannoLocation
jSite :: Maybe JannoSite
jLatitude :: Maybe JannoLatitude
jLongitude :: Maybe JannoLongitude
jDateType :: Maybe JannoDateType
jDateC14Labnr :: Maybe (ListColumn JannoDateC14Labnr)
jDateC14UncalBP :: Maybe (ListColumn JannoDateC14UncalBP)
jDateC14UncalBPErr :: Maybe (ListColumn JannoDateC14UncalBPErr)
jDateBCADStart :: Maybe JannoDateBCADStart
jDateBCADMedian :: Maybe JannoDateBCADMedian
jDateBCADStop :: Maybe JannoDateBCADStop
jDateNote :: Maybe JannoDateNote
jMTHaplogroup :: Maybe JannoMTHaplogroup
jYHaplogroup :: Maybe JannoYHaplogroup
jSourceTissue :: Maybe (ListColumn JannoSourceTissue)
jNrLibraries :: Maybe JannoNrLibraries
jLibraryNames :: Maybe (ListColumn JannoLibraryName)
jCaptureType :: Maybe (ListColumn JannoCaptureType)
jUDG :: Maybe JannoUDG
jLibraryBuilt :: Maybe JannoLibraryBuilt
jGenotypePloidy :: Maybe JannoGenotypePloidy
jDataPreparationPipelineURL :: Maybe JannoDataPreparationPipelineURL
jEndogenous :: Maybe JannoEndogenous
jNrSNPs :: Maybe JannoNrSNPs
jCoverageOnTargets :: Maybe JannoCoverageOnTargets
jDamage :: Maybe JannoDamage
jContamination :: Maybe (ListColumn JannoContamination)
jContaminationErr :: Maybe (ListColumn JannoContaminationErr)
jContaminationMeas :: Maybe (ListColumn JannoContaminationMeas)
jContaminationNote :: Maybe JannoContaminationNote
jGeneticSourceAccessionIDs :: Maybe (ListColumn JannoGeneticSourceAccessionID)
jPrimaryContact :: Maybe JannoPrimaryContact
jPublication :: Maybe (ListColumn JannoPublication)
jComments :: Maybe JannoComment
jKeywords :: Maybe (ListColumn JannoKeyword)
jAdditionalColumns :: CsvNamedRecord

Instances

Instances details

Generic JannoRow Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoRow :: Type -> Type # Methods from :: JannoRow -> Rep JannoRow x # to :: Rep JannoRow x -> JannoRow #
Show JannoRow Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoRow -> ShowS # show :: JannoRow -> String # showList :: [JannoRow] -> ShowS #
DefaultOrdered JannoRow Source #
Instance details Defined in Poseidon.Janno Methods headerOrder :: JannoRow -> Header
FromNamedRecord JannoRow Source #
Instance details Defined in Poseidon.Janno Methods parseNamedRecord :: NamedRecord -> Parser JannoRow
ToNamedRecord JannoRow Source #
Instance details Defined in Poseidon.Janno Methods toNamedRecord :: JannoRow -> NamedRecord
Generic JannoRow Source #
Instance details Defined in Poseidon.Janno Associated Types type Code JannoRow :: [[Type]] Methods from :: JannoRow -> Rep JannoRow to :: Rep JannoRow -> JannoRow
HasDatatypeInfo JannoRow Source #
Instance details Defined in Poseidon.Janno Associated Types type DatatypeInfoOf JannoRow :: DatatypeInfo Methods datatypeInfo :: proxy JannoRow -> DatatypeInfo (Code JannoRow)
Eq JannoRow Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoRow -> JannoRow -> Bool # (/=) :: JannoRow -> JannoRow -> Bool #
type Rep JannoRow Source #
Instance details Defined in Poseidon.Janno type Rep JannoRow = D1 ('MetaData "JannoRow" "Poseidon.Janno" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) (C1 ('MetaCons "JannoRow" 'PrefixI 'True) (((((S1 ('MetaSel ('Just "jPoseidonID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 String) :: S1 ('MetaSel ('Just "jGeneticSex") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 GeneticSex)) :: (S1 ('MetaSel ('Just "jGroupName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (ListColumn GroupName)) :: (S1 ('MetaSel ('Just "jAlternativeIDs") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoAlternativeID))) :: S1 ('MetaSel ('Just "jRelationTo") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoRelationTo)))))) :: ((S1 ('MetaSel ('Just "jRelationDegree") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoRelationDegree))) :: (S1 ('MetaSel ('Just "jRelationType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoRelationType))) :: S1 ('MetaSel ('Just "jRelationNote") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoRelationNote)))) :: (S1 ('MetaSel ('Just "jCollectionID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoCollectionID)) :: (S1 ('MetaSel ('Just "jCountry") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoCountry)) :: S1 ('MetaSel ('Just "jCountryISO") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoCountryISO)))))) :: (((S1 ('MetaSel ('Just "jLocation") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoLocation)) :: (S1 ('MetaSel ('Just "jSite") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoSite)) :: S1 ('MetaSel ('Just "jLatitude") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoLatitude)))) :: (S1 ('MetaSel ('Just "jLongitude") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoLongitude)) :: (S1 ('MetaSel ('Just "jDateType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDateType)) :: S1 ('MetaSel ('Just "jDateC14Labnr") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoDateC14Labnr)))))) :: ((S1 ('MetaSel ('Just "jDateC14UncalBP") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoDateC14UncalBP))) :: (S1 ('MetaSel ('Just "jDateC14UncalBPErr") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoDateC14UncalBPErr))) :: S1 ('MetaSel ('Just "jDateBCADStart") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDateBCADStart)))) :: (S1 ('MetaSel ('Just "jDateBCADMedian") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDateBCADMedian)) :: (S1 ('MetaSel ('Just "jDateBCADStop") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDateBCADStop)) :: S1 ('MetaSel ('Just "jDateNote") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDateNote))))))) :: ((((S1 ('MetaSel ('Just "jMTHaplogroup") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoMTHaplogroup)) :: (S1 ('MetaSel ('Just "jYHaplogroup") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoYHaplogroup)) :: S1 ('MetaSel ('Just "jSourceTissue") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoSourceTissue))))) :: (S1 ('MetaSel ('Just "jNrLibraries") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoNrLibraries)) :: (S1 ('MetaSel ('Just "jLibraryNames") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoLibraryName))) :: S1 ('MetaSel ('Just "jCaptureType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoCaptureType)))))) :: ((S1 ('MetaSel ('Just "jUDG") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoUDG)) :: (S1 ('MetaSel ('Just "jLibraryBuilt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoLibraryBuilt)) :: S1 ('MetaSel ('Just "jGenotypePloidy") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoGenotypePloidy)))) :: (S1 ('MetaSel ('Just "jDataPreparationPipelineURL") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDataPreparationPipelineURL)) :: (S1 ('MetaSel ('Just "jEndogenous") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoEndogenous)) :: S1 ('MetaSel ('Just "jNrSNPs") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoNrSNPs)))))) :: (((S1 ('MetaSel ('Just "jCoverageOnTargets") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoCoverageOnTargets)) :: (S1 ('MetaSel ('Just "jDamage") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoDamage)) :: S1 ('MetaSel ('Just "jContamination") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoContamination))))) :: (S1 ('MetaSel ('Just "jContaminationErr") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoContaminationErr))) :: (S1 ('MetaSel ('Just "jContaminationMeas") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoContaminationMeas))) :: S1 ('MetaSel ('Just "jContaminationNote") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoContaminationNote))))) :: ((S1 ('MetaSel ('Just "jGeneticSourceAccessionIDs") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoGeneticSourceAccessionID))) :: (S1 ('MetaSel ('Just "jPrimaryContact") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoPrimaryContact)) :: S1 ('MetaSel ('Just "jPublication") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoPublication))))) :: (S1 ('MetaSel ('Just "jComments") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe JannoComment)) :: (S1 ('MetaSel ('Just "jKeywords") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (ListColumn JannoKeyword))) :: S1 ('MetaSel ('Just "jAdditionalColumns") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 CsvNamedRecord))))))))
type Code JannoRow Source #
Instance details Defined in Poseidon.Janno type Code JannoRow = '['[String, GeneticSex, ListColumn GroupName, Maybe (ListColumn JannoAlternativeID), Maybe (ListColumn JannoRelationTo), Maybe (ListColumn JannoRelationDegree), Maybe (ListColumn JannoRelationType), Maybe JannoRelationNote, Maybe JannoCollectionID, Maybe JannoCountry, Maybe JannoCountryISO, Maybe JannoLocation, Maybe JannoSite, Maybe JannoLatitude, Maybe JannoLongitude, Maybe JannoDateType, Maybe (ListColumn JannoDateC14Labnr), Maybe (ListColumn JannoDateC14UncalBP), Maybe (ListColumn JannoDateC14UncalBPErr), Maybe JannoDateBCADStart, Maybe JannoDateBCADMedian, Maybe JannoDateBCADStop, Maybe JannoDateNote, Maybe JannoMTHaplogroup, Maybe JannoYHaplogroup, Maybe (ListColumn JannoSourceTissue), Maybe JannoNrLibraries, Maybe (ListColumn JannoLibraryName), Maybe (ListColumn JannoCaptureType), Maybe JannoUDG, Maybe JannoLibraryBuilt, Maybe JannoGenotypePloidy, Maybe JannoDataPreparationPipelineURL, Maybe JannoEndogenous, Maybe JannoNrSNPs, Maybe JannoCoverageOnTargets, Maybe JannoDamage, Maybe (ListColumn JannoContamination), Maybe (ListColumn JannoContaminationErr), Maybe (ListColumn JannoContaminationMeas), Maybe JannoContaminationNote, Maybe (ListColumn JannoGeneticSourceAccessionID), Maybe JannoPrimaryContact, Maybe (ListColumn JannoPublication), Maybe JannoComment, Maybe (ListColumn JannoKeyword), CsvNamedRecord]]
type DatatypeInfoOf JannoRow Source #
Instance details Defined in Poseidon.Janno type DatatypeInfoOf JannoRow = 'ADT "Poseidon.Janno" "JannoRow" '['Record "JannoRow" '['FieldInfo "jPoseidonID", 'FieldInfo "jGeneticSex", 'FieldInfo "jGroupName", 'FieldInfo "jAlternativeIDs", 'FieldInfo "jRelationTo", 'FieldInfo "jRelationDegree", 'FieldInfo "jRelationType", 'FieldInfo "jRelationNote", 'FieldInfo "jCollectionID", 'FieldInfo "jCountry", 'FieldInfo "jCountryISO", 'FieldInfo "jLocation", 'FieldInfo "jSite", 'FieldInfo "jLatitude", 'FieldInfo "jLongitude", 'FieldInfo "jDateType", 'FieldInfo "jDateC14Labnr", 'FieldInfo "jDateC14UncalBP", 'FieldInfo "jDateC14UncalBPErr", 'FieldInfo "jDateBCADStart", 'FieldInfo "jDateBCADMedian", 'FieldInfo "jDateBCADStop", 'FieldInfo "jDateNote", 'FieldInfo "jMTHaplogroup", 'FieldInfo "jYHaplogroup", 'FieldInfo "jSourceTissue", 'FieldInfo "jNrLibraries", 'FieldInfo "jLibraryNames", 'FieldInfo "jCaptureType", 'FieldInfo "jUDG", 'FieldInfo "jLibraryBuilt", 'FieldInfo "jGenotypePloidy", 'FieldInfo "jDataPreparationPipelineURL", 'FieldInfo "jEndogenous", 'FieldInfo "jNrSNPs", 'FieldInfo "jCoverageOnTargets", 'FieldInfo "jDamage", 'FieldInfo "jContamination", 'FieldInfo "jContaminationErr", 'FieldInfo "jContaminationMeas", 'FieldInfo "jContaminationNote", 'FieldInfo "jGeneticSourceAccessionIDs", 'FieldInfo "jPrimaryContact", 'FieldInfo "jPublication", 'FieldInfo "jComments", 'FieldInfo "jKeywords", 'FieldInfo "jAdditionalColumns"]] '['['StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy, 'StrictnessInfo 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy]]

newtype GeneticSex Source #

A datatype for the Genetic_Sex .janno column

Constructors

GeneticSex
Fields sfSex :: Sex

Instances

Instances details

Show GeneticSex Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> GeneticSex -> ShowS # show :: GeneticSex -> String # showList :: [GeneticSex] -> ShowS #
FromField GeneticSex Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser GeneticSex
ToField GeneticSex Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: GeneticSex -> Field
Eq GeneticSex Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: GeneticSex -> GeneticSex -> Bool # (/=) :: GeneticSex -> GeneticSex -> Bool #
Ord GeneticSex Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: GeneticSex -> GeneticSex -> Ordering # (<) :: GeneticSex -> GeneticSex -> Bool # (<=) :: GeneticSex -> GeneticSex -> Bool # (>) :: GeneticSex -> GeneticSex -> Bool # (>=) :: GeneticSex -> GeneticSex -> Bool # max :: GeneticSex -> GeneticSex -> GeneticSex # min :: GeneticSex -> GeneticSex -> GeneticSex #
PresenceCountable GeneticSex Source #
Instance details Defined in Poseidon.CLI.Survey Methods countPresence :: GeneticSex -> Int Source #
Makeable GeneticSex Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m GeneticSex Source #

newtype GroupName Source #

A datatype for the Group_Name .janno column

Constructors

GroupName Text

Instances

Instances details

Show GroupName Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> GroupName -> ShowS # show :: GroupName -> String # showList :: [GroupName] -> ShowS #
FromField GroupName Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser GroupName
ToField GroupName Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: GroupName -> Field
Eq GroupName Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: GroupName -> GroupName -> Bool # (/=) :: GroupName -> GroupName -> Bool #
Ord GroupName Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: GroupName -> GroupName -> Ordering # (<) :: GroupName -> GroupName -> Bool # (<=) :: GroupName -> GroupName -> Bool # (>) :: GroupName -> GroupName -> Bool # (>=) :: GroupName -> GroupName -> Bool # max :: GroupName -> GroupName -> GroupName # min :: GroupName -> GroupName -> GroupName #
Makeable GroupName Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m GroupName Source #

newtype ListColumn a Source #

A general datatype for janno list columns

Constructors

ListColumn
Fields getListColumn :: [a]

Instances

Instances details

Generic (ListColumn a) Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep (ListColumn a) :: Type -> Type # Methods from :: ListColumn a -> Rep (ListColumn a) x # to :: Rep (ListColumn a) x -> ListColumn a #
Show a => Show (ListColumn a) Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> ListColumn a -> ShowS # show :: ListColumn a -> String # showList :: [ListColumn a] -> ShowS #
FromField a => FromField (ListColumn a) Source #
Instance details Defined in Poseidon.Janno Methods parseField :: Field -> Parser (ListColumn a)
(ToField a, Show a) => ToField (ListColumn a) Source #
Instance details Defined in Poseidon.Janno Methods toField :: ListColumn a -> Field
Eq a => Eq (ListColumn a) Source #
Instance details Defined in Poseidon.Janno Methods (==) :: ListColumn a -> ListColumn a -> Bool # (/=) :: ListColumn a -> ListColumn a -> Bool #
Ord a => Ord (ListColumn a) Source #
Instance details Defined in Poseidon.Janno Methods compare :: ListColumn a -> ListColumn a -> Ordering # (<) :: ListColumn a -> ListColumn a -> Bool # (<=) :: ListColumn a -> ListColumn a -> Bool # (>) :: ListColumn a -> ListColumn a -> Bool # (>=) :: ListColumn a -> ListColumn a -> Bool # max :: ListColumn a -> ListColumn a -> ListColumn a # min :: ListColumn a -> ListColumn a -> ListColumn a #
PresenceCountable (ListColumn a) Source #
Instance details Defined in Poseidon.CLI.Survey Methods countPresence :: ListColumn a -> Int Source #
type Rep (ListColumn a) Source #
Instance details Defined in Poseidon.Janno type Rep (ListColumn a) = D1 ('MetaData "ListColumn" "Poseidon.Janno" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'True) (C1 ('MetaCons "ListColumn" 'PrefixI 'True) (S1 ('MetaSel ('Just "getListColumn") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [a])))

data Sex #

Constructors

Male
Female
Unknown

Instances

Instances details

Show Sex
Instance details Defined in SequenceFormats.Eigenstrat Methods showsPrec :: Int -> Sex -> ShowS # show :: Sex -> String # showList :: [Sex] -> ShowS #
Eq Sex
Instance details Defined in SequenceFormats.Eigenstrat Methods (==) :: Sex -> Sex -> Bool # (/=) :: Sex -> Sex -> Bool #

newtype JannoCountryISO Source #

A datatype for countries in ISO-alpha2 code format

Constructors

JannoCountryISO Country

Instances

Instances details

Show JannoCountryISO Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoCountryISO -> ShowS # show :: JannoCountryISO -> String # showList :: [JannoCountryISO] -> ShowS #
FromField JannoCountryISO Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoCountryISO
ToField JannoCountryISO Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoCountryISO -> Field
Eq JannoCountryISO Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoCountryISO -> JannoCountryISO -> Bool # (/=) :: JannoCountryISO -> JannoCountryISO -> Bool #
Ord JannoCountryISO Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoCountryISO -> JannoCountryISO -> Ordering # (<) :: JannoCountryISO -> JannoCountryISO -> Bool # (<=) :: JannoCountryISO -> JannoCountryISO -> Bool # (>) :: JannoCountryISO -> JannoCountryISO -> Bool # (>=) :: JannoCountryISO -> JannoCountryISO -> Bool # max :: JannoCountryISO -> JannoCountryISO -> JannoCountryISO # min :: JannoCountryISO -> JannoCountryISO -> JannoCountryISO #
Makeable JannoCountryISO Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoCountryISO Source #

newtype JannoLatitude Source #

A datatype for the Latitude .janno column

Constructors

JannoLatitude Double

Instances

Instances details

Generic JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoLatitude :: Type -> Type # Methods from :: JannoLatitude -> Rep JannoLatitude x # to :: Rep JannoLatitude x -> JannoLatitude #
Show JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoLatitude -> ShowS # show :: JannoLatitude -> String # showList :: [JannoLatitude] -> ShowS #
FromField JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoLatitude
ToField JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoLatitude -> Field
Eq JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoLatitude -> JannoLatitude -> Bool # (/=) :: JannoLatitude -> JannoLatitude -> Bool #
Ord JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoLatitude -> JannoLatitude -> Ordering # (<) :: JannoLatitude -> JannoLatitude -> Bool # (<=) :: JannoLatitude -> JannoLatitude -> Bool # (>) :: JannoLatitude -> JannoLatitude -> Bool # (>=) :: JannoLatitude -> JannoLatitude -> Bool # max :: JannoLatitude -> JannoLatitude -> JannoLatitude # min :: JannoLatitude -> JannoLatitude -> JannoLatitude #
Makeable JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoLatitude Source #
type Rep JannoLatitude Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoLatitude = D1 ('MetaData "JannoLatitude" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'True) (C1 ('MetaCons "JannoLatitude" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

newtype JannoLongitude Source #

A datatype for the Longitude .janno column

Constructors

JannoLongitude Double

Instances

Instances details

Generic JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoLongitude :: Type -> Type # Methods from :: JannoLongitude -> Rep JannoLongitude x # to :: Rep JannoLongitude x -> JannoLongitude #
Show JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoLongitude -> ShowS # show :: JannoLongitude -> String # showList :: [JannoLongitude] -> ShowS #
FromField JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoLongitude
ToField JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoLongitude -> Field
Eq JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoLongitude -> JannoLongitude -> Bool # (/=) :: JannoLongitude -> JannoLongitude -> Bool #
Ord JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoLongitude -> JannoLongitude -> Ordering # (<) :: JannoLongitude -> JannoLongitude -> Bool # (<=) :: JannoLongitude -> JannoLongitude -> Bool # (>) :: JannoLongitude -> JannoLongitude -> Bool # (>=) :: JannoLongitude -> JannoLongitude -> Bool # max :: JannoLongitude -> JannoLongitude -> JannoLongitude # min :: JannoLongitude -> JannoLongitude -> JannoLongitude #
Makeable JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoLongitude Source #
type Rep JannoLongitude Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoLongitude = D1 ('MetaData "JannoLongitude" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'True) (C1 ('MetaCons "JannoLongitude" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

data JannoDateType Source #

A datatype for the Date_Type .janno column

Constructors

C14
Contextual
Modern

Instances

Instances details

Bounded JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods minBound :: JannoDateType # maxBound :: JannoDateType #
Enum JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods succ :: JannoDateType -> JannoDateType # pred :: JannoDateType -> JannoDateType # toEnum :: Int -> JannoDateType # fromEnum :: JannoDateType -> Int # enumFrom :: JannoDateType -> [JannoDateType] # enumFromThen :: JannoDateType -> JannoDateType -> [JannoDateType] # enumFromTo :: JannoDateType -> JannoDateType -> [JannoDateType] # enumFromThenTo :: JannoDateType -> JannoDateType -> JannoDateType -> [JannoDateType] #
Generic JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoDateType :: Type -> Type # Methods from :: JannoDateType -> Rep JannoDateType x # to :: Rep JannoDateType x -> JannoDateType #
Show JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoDateType -> ShowS # show :: JannoDateType -> String # showList :: [JannoDateType] -> ShowS #
FromField JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoDateType
ToField JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoDateType -> Field
Eq JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoDateType -> JannoDateType -> Bool # (/=) :: JannoDateType -> JannoDateType -> Bool #
Ord JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoDateType -> JannoDateType -> Ordering # (<) :: JannoDateType -> JannoDateType -> Bool # (<=) :: JannoDateType -> JannoDateType -> Bool # (>) :: JannoDateType -> JannoDateType -> Bool # (>=) :: JannoDateType -> JannoDateType -> Bool # max :: JannoDateType -> JannoDateType -> JannoDateType # min :: JannoDateType -> JannoDateType -> JannoDateType #
Makeable JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoDateType Source #
type Rep JannoDateType Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoDateType = D1 ('MetaData "JannoDateType" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) (C1 ('MetaCons "C14" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Contextual" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Modern" 'PrefixI 'False) (U1 :: Type -> Type)))

newtype JannoDateBCADMedian Source #

A datatype for the Date_BC_AD_Median .janno column

Constructors

JannoDateBCADMedian Int

Instances

Instances details

Generic JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoDateBCADMedian :: Type -> Type # Methods from :: JannoDateBCADMedian -> Rep JannoDateBCADMedian x # to :: Rep JannoDateBCADMedian x -> JannoDateBCADMedian #
Show JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoDateBCADMedian -> ShowS # show :: JannoDateBCADMedian -> String # showList :: [JannoDateBCADMedian] -> ShowS #
FromField JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoDateBCADMedian
ToField JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoDateBCADMedian -> Field
Eq JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoDateBCADMedian -> JannoDateBCADMedian -> Bool # (/=) :: JannoDateBCADMedian -> JannoDateBCADMedian -> Bool #
Ord JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoDateBCADMedian -> JannoDateBCADMedian -> Ordering # (<) :: JannoDateBCADMedian -> JannoDateBCADMedian -> Bool # (<=) :: JannoDateBCADMedian -> JannoDateBCADMedian -> Bool # (>) :: JannoDateBCADMedian -> JannoDateBCADMedian -> Bool # (>=) :: JannoDateBCADMedian -> JannoDateBCADMedian -> Bool # max :: JannoDateBCADMedian -> JannoDateBCADMedian -> JannoDateBCADMedian # min :: JannoDateBCADMedian -> JannoDateBCADMedian -> JannoDateBCADMedian #
Makeable JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoDateBCADMedian Source #
type Rep JannoDateBCADMedian Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoDateBCADMedian = D1 ('MetaData "JannoDateBCADMedian" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'True) (C1 ('MetaCons "JannoDateBCADMedian" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))

data JannoCaptureType Source #

A datatype for the Capture_Type .janno column

Constructors

Shotgun
A1240K
ArborComplete
ArborPrimePlus
ArborAncestralPlus
TwistAncientDNA
OtherCapture
ReferenceGenome

Instances

Instances details

Bounded JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods minBound :: JannoCaptureType # maxBound :: JannoCaptureType #
Enum JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods succ :: JannoCaptureType -> JannoCaptureType # pred :: JannoCaptureType -> JannoCaptureType # toEnum :: Int -> JannoCaptureType # fromEnum :: JannoCaptureType -> Int # enumFrom :: JannoCaptureType -> [JannoCaptureType] # enumFromThen :: JannoCaptureType -> JannoCaptureType -> [JannoCaptureType] # enumFromTo :: JannoCaptureType -> JannoCaptureType -> [JannoCaptureType] # enumFromThenTo :: JannoCaptureType -> JannoCaptureType -> JannoCaptureType -> [JannoCaptureType] #
Generic JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoCaptureType :: Type -> Type # Methods from :: JannoCaptureType -> Rep JannoCaptureType x # to :: Rep JannoCaptureType x -> JannoCaptureType #
Show JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoCaptureType -> ShowS # show :: JannoCaptureType -> String # showList :: [JannoCaptureType] -> ShowS #
FromField JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoCaptureType
ToField JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoCaptureType -> Field
Eq JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoCaptureType -> JannoCaptureType -> Bool # (/=) :: JannoCaptureType -> JannoCaptureType -> Bool #
Ord JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoCaptureType -> JannoCaptureType -> Ordering # (<) :: JannoCaptureType -> JannoCaptureType -> Bool # (<=) :: JannoCaptureType -> JannoCaptureType -> Bool # (>) :: JannoCaptureType -> JannoCaptureType -> Bool # (>=) :: JannoCaptureType -> JannoCaptureType -> Bool # max :: JannoCaptureType -> JannoCaptureType -> JannoCaptureType # min :: JannoCaptureType -> JannoCaptureType -> JannoCaptureType #
Makeable JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoCaptureType Source #
type Rep JannoCaptureType Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoCaptureType = D1 ('MetaData "JannoCaptureType" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) (((C1 ('MetaCons "Shotgun" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "A1240K" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "ArborComplete" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ArborPrimePlus" 'PrefixI 'False) (U1 :: Type -> Type))) :+: ((C1 ('MetaCons "ArborAncestralPlus" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "TwistAncientDNA" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "OtherCapture" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ReferenceGenome" 'PrefixI 'False) (U1 :: Type -> Type))))

data JannoGenotypePloidy Source #

A datatype for the Genotype_Ploidy .janno column

Constructors

Diploid
Haploid

Instances

Instances details

Bounded JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods minBound :: JannoGenotypePloidy # maxBound :: JannoGenotypePloidy #
Enum JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods succ :: JannoGenotypePloidy -> JannoGenotypePloidy # pred :: JannoGenotypePloidy -> JannoGenotypePloidy # toEnum :: Int -> JannoGenotypePloidy # fromEnum :: JannoGenotypePloidy -> Int # enumFrom :: JannoGenotypePloidy -> [JannoGenotypePloidy] # enumFromThen :: JannoGenotypePloidy -> JannoGenotypePloidy -> [JannoGenotypePloidy] # enumFromTo :: JannoGenotypePloidy -> JannoGenotypePloidy -> [JannoGenotypePloidy] # enumFromThenTo :: JannoGenotypePloidy -> JannoGenotypePloidy -> JannoGenotypePloidy -> [JannoGenotypePloidy] #
Generic JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoGenotypePloidy :: Type -> Type # Methods from :: JannoGenotypePloidy -> Rep JannoGenotypePloidy x # to :: Rep JannoGenotypePloidy x -> JannoGenotypePloidy #
Show JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoGenotypePloidy -> ShowS # show :: JannoGenotypePloidy -> String # showList :: [JannoGenotypePloidy] -> ShowS #
FromField JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoGenotypePloidy
ToField JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoGenotypePloidy -> Field
Eq JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (/=) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool #
Ord JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoGenotypePloidy -> JannoGenotypePloidy -> Ordering # (<) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (<=) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (>) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # (>=) :: JannoGenotypePloidy -> JannoGenotypePloidy -> Bool # max :: JannoGenotypePloidy -> JannoGenotypePloidy -> JannoGenotypePloidy # min :: JannoGenotypePloidy -> JannoGenotypePloidy -> JannoGenotypePloidy #
Makeable JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoGenotypePloidy Source #
type Rep JannoGenotypePloidy Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoGenotypePloidy = D1 ('MetaData "JannoGenotypePloidy" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) (C1 ('MetaCons "Diploid" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Haploid" 'PrefixI 'False) (U1 :: Type -> Type))

data JannoUDG Source #

A datatype for the UDG .janno column

Constructors

Minus
Half
Plus
Mixed

Instances

Instances details

Bounded JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods minBound :: JannoUDG # maxBound :: JannoUDG #
Enum JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods succ :: JannoUDG -> JannoUDG # pred :: JannoUDG -> JannoUDG # toEnum :: Int -> JannoUDG # fromEnum :: JannoUDG -> Int # enumFrom :: JannoUDG -> [JannoUDG] # enumFromThen :: JannoUDG -> JannoUDG -> [JannoUDG] # enumFromTo :: JannoUDG -> JannoUDG -> [JannoUDG] # enumFromThenTo :: JannoUDG -> JannoUDG -> JannoUDG -> [JannoUDG] #
Generic JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoUDG :: Type -> Type # Methods from :: JannoUDG -> Rep JannoUDG x # to :: Rep JannoUDG x -> JannoUDG #
Show JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoUDG -> ShowS # show :: JannoUDG -> String # showList :: [JannoUDG] -> ShowS #
FromField JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoUDG
ToField JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoUDG -> Field
Eq JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoUDG -> JannoUDG -> Bool # (/=) :: JannoUDG -> JannoUDG -> Bool #
Ord JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoUDG -> JannoUDG -> Ordering # (<) :: JannoUDG -> JannoUDG -> Bool # (<=) :: JannoUDG -> JannoUDG -> Bool # (>) :: JannoUDG -> JannoUDG -> Bool # (>=) :: JannoUDG -> JannoUDG -> Bool # max :: JannoUDG -> JannoUDG -> JannoUDG # min :: JannoUDG -> JannoUDG -> JannoUDG #
Makeable JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoUDG Source #
type Rep JannoUDG Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoUDG = D1 ('MetaData "JannoUDG" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) ((C1 ('MetaCons "Minus" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Half" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Plus" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Mixed" 'PrefixI 'False) (U1 :: Type -> Type)))

data JannoRelationDegree Source #

A datatype for the Relation_Degree .janno column

Constructors

Identical
First
Second
ThirdToFifth
SixthToTenth
Unrelated
OtherDegree

Instances

Instances details

Bounded JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods minBound :: JannoRelationDegree # maxBound :: JannoRelationDegree #
Enum JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods succ :: JannoRelationDegree -> JannoRelationDegree # pred :: JannoRelationDegree -> JannoRelationDegree # toEnum :: Int -> JannoRelationDegree # fromEnum :: JannoRelationDegree -> Int # enumFrom :: JannoRelationDegree -> [JannoRelationDegree] # enumFromThen :: JannoRelationDegree -> JannoRelationDegree -> [JannoRelationDegree] # enumFromTo :: JannoRelationDegree -> JannoRelationDegree -> [JannoRelationDegree] # enumFromThenTo :: JannoRelationDegree -> JannoRelationDegree -> JannoRelationDegree -> [JannoRelationDegree] #
Generic JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoRelationDegree :: Type -> Type # Methods from :: JannoRelationDegree -> Rep JannoRelationDegree x # to :: Rep JannoRelationDegree x -> JannoRelationDegree #
Show JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoRelationDegree -> ShowS # show :: JannoRelationDegree -> String # showList :: [JannoRelationDegree] -> ShowS #
FromField JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoRelationDegree
ToField JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoRelationDegree -> Field
Eq JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoRelationDegree -> JannoRelationDegree -> Bool # (/=) :: JannoRelationDegree -> JannoRelationDegree -> Bool #
Ord JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoRelationDegree -> JannoRelationDegree -> Ordering # (<) :: JannoRelationDegree -> JannoRelationDegree -> Bool # (<=) :: JannoRelationDegree -> JannoRelationDegree -> Bool # (>) :: JannoRelationDegree -> JannoRelationDegree -> Bool # (>=) :: JannoRelationDegree -> JannoRelationDegree -> Bool # max :: JannoRelationDegree -> JannoRelationDegree -> JannoRelationDegree # min :: JannoRelationDegree -> JannoRelationDegree -> JannoRelationDegree #
Makeable JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoRelationDegree Source #
type Rep JannoRelationDegree Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoRelationDegree = D1 ('MetaData "JannoRelationDegree" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) ((C1 ('MetaCons "Identical" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "First" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Second" 'PrefixI 'False) (U1 :: Type -> Type))) :+: ((C1 ('MetaCons "ThirdToFifth" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SixthToTenth" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Unrelated" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "OtherDegree" 'PrefixI 'False) (U1 :: Type -> Type))))

data JannoLibraryBuilt Source #

A datatype for the Library_Built .janno column

Constructors

DS
SS
MixedSSDS
Other

Instances

Instances details

Bounded JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods minBound :: JannoLibraryBuilt # maxBound :: JannoLibraryBuilt #
Enum JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods succ :: JannoLibraryBuilt -> JannoLibraryBuilt # pred :: JannoLibraryBuilt -> JannoLibraryBuilt # toEnum :: Int -> JannoLibraryBuilt # fromEnum :: JannoLibraryBuilt -> Int # enumFrom :: JannoLibraryBuilt -> [JannoLibraryBuilt] # enumFromThen :: JannoLibraryBuilt -> JannoLibraryBuilt -> [JannoLibraryBuilt] # enumFromTo :: JannoLibraryBuilt -> JannoLibraryBuilt -> [JannoLibraryBuilt] # enumFromThenTo :: JannoLibraryBuilt -> JannoLibraryBuilt -> JannoLibraryBuilt -> [JannoLibraryBuilt] #
Generic JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Associated Types type Rep JannoLibraryBuilt :: Type -> Type # Methods from :: JannoLibraryBuilt -> Rep JannoLibraryBuilt x # to :: Rep JannoLibraryBuilt x -> JannoLibraryBuilt #
Show JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods showsPrec :: Int -> JannoLibraryBuilt -> ShowS # show :: JannoLibraryBuilt -> String # showList :: [JannoLibraryBuilt] -> ShowS #
FromField JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods parseField :: Field -> Parser JannoLibraryBuilt
ToField JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods toField :: JannoLibraryBuilt -> Field
Eq JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods (==) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (/=) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool #
Ord JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods compare :: JannoLibraryBuilt -> JannoLibraryBuilt -> Ordering # (<) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (<=) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (>) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # (>=) :: JannoLibraryBuilt -> JannoLibraryBuilt -> Bool # max :: JannoLibraryBuilt -> JannoLibraryBuilt -> JannoLibraryBuilt # min :: JannoLibraryBuilt -> JannoLibraryBuilt -> JannoLibraryBuilt #
Makeable JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes Methods make :: MonadFail m => Text -> m JannoLibraryBuilt Source #
type Rep JannoLibraryBuilt Source #
Instance details Defined in Poseidon.ColumnTypes type Rep JannoLibraryBuilt = D1 ('MetaData "JannoLibraryBuilt" "Poseidon.ColumnTypes" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'False) ((C1 ('MetaCons "DS" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SS" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "MixedSSDS" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Other" 'PrefixI 'False) (U1 :: Type -> Type)))

writeJannoFile :: FilePath -> JannoRows -> IO () Source #

writeJannoFileWithoutEmptyCols :: FilePath -> JannoRows -> IO () Source #

readJannoFile :: FilePath -> PoseidonIO JannoRows Source #

A function to load one janno file

createMinimalJanno :: [EigenstratIndEntry] -> JannoRows Source #

A function to create empty janno rows for a set of individuals

createMinimalSample :: EigenstratIndEntry -> JannoRow Source #

A function to create an empty janno row for an individual

jannoHeaderString :: [String] Source #

newtype CsvNamedRecord Source #

A datatype to collect additional, unpecified .janno file columns (a hashmap in cassava/Data.Csv)

Constructors

CsvNamedRecord NamedRecord

Instances

Instances details

Generic CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep CsvNamedRecord :: Type -> Type # Methods from :: CsvNamedRecord -> Rep CsvNamedRecord x # to :: Rep CsvNamedRecord x -> CsvNamedRecord #
Show CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> CsvNamedRecord -> ShowS # show :: CsvNamedRecord -> String # showList :: [CsvNamedRecord] -> ShowS #
Eq CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno Methods (==) :: CsvNamedRecord -> CsvNamedRecord -> Bool # (/=) :: CsvNamedRecord -> CsvNamedRecord -> Bool #
PresenceCountable CsvNamedRecord Source #
Instance details Defined in Poseidon.CLI.Survey Methods countPresence :: CsvNamedRecord -> Int Source #
type Rep CsvNamedRecord Source #
Instance details Defined in Poseidon.Janno type Rep CsvNamedRecord = D1 ('MetaData "CsvNamedRecord" "Poseidon.Janno" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'True) (C1 ('MetaCons "CsvNamedRecord" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 NamedRecord)))

newtype JannoRows Source #

A data type to represent a janno file

Constructors

JannoRows
Fields getJannoRows :: [JannoRow]

Instances

Instances details

Monoid JannoRows Source #
Instance details Defined in Poseidon.Janno Methods mempty :: JannoRows # mappend :: JannoRows -> JannoRows -> JannoRows # mconcat :: [JannoRows] -> JannoRows #
Semigroup JannoRows Source #
Instance details Defined in Poseidon.Janno Methods (<>) :: JannoRows -> JannoRows -> JannoRows # sconcat :: NonEmpty JannoRows -> JannoRows # stimes :: Integral b => b -> JannoRows -> JannoRows #
Generic JannoRows Source #
Instance details Defined in Poseidon.Janno Associated Types type Rep JannoRows :: Type -> Type # Methods from :: JannoRows -> Rep JannoRows x # to :: Rep JannoRows x -> JannoRows #
Show JannoRows Source #
Instance details Defined in Poseidon.Janno Methods showsPrec :: Int -> JannoRows -> ShowS # show :: JannoRows -> String # showList :: [JannoRows] -> ShowS #
Eq JannoRows Source #
Instance details Defined in Poseidon.Janno Methods (==) :: JannoRows -> JannoRows -> Bool # (/=) :: JannoRows -> JannoRows -> Bool #
type Rep JannoRows Source #
Instance details Defined in Poseidon.Janno type Rep JannoRows = D1 ('MetaData "JannoRows" "Poseidon.Janno" "poseidon-hs-1.6.3.0-D86RdwVZjl0EE9ZYqAyXfe" 'True) (C1 ('MetaCons "JannoRows" 'PrefixI 'True) (S1 ('MetaSel ('Just "getJannoRows") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [JannoRow])))

type JannoStringList = ListColumn String Source #

filterLookup :: FromField a => NamedRecord -> ByteString -> Parser a Source #

filterLookupOptional :: FromField a => NamedRecord -> ByteString -> Parser (Maybe a) Source #

getCsvNR :: CsvNamedRecord -> NamedRecord Source #

encodingOptions :: EncodeOptions Source #

decodingOptions :: DecodeOptions Source #

explicitNA :: NamedRecord -> NamedRecord Source #

removeUselessSuffix :: String -> String Source #

parseCsvParseError :: Parser CsvParseError Source #

renderCsvParseError :: CsvParseError -> String Source #

getMaybeListColumn :: Maybe (ListColumn a) -> [a] Source #

jannoRows2EigenstratIndEntries :: JannoRows -> [EigenstratIndEntry] Source #

a convenience function to construct Eigenstrat Ind entries out of jannoRows

makeHeaderWithAdditionalColumns :: [JannoRow] -> Header Source #