poseidon-hs-1.6.7.3: A package with tools for working with Poseidon genotype data
Safe HaskellSafe-Inferred
LanguageHaskell2010

Poseidon.ColumnTypesUtils

Synopsis

Documentation

class Makeable a where Source #

Methods

make :: MonadFail m => Text -> m a Source #

Instances

Instances details
Makeable GeneticSex Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m GeneticSex Source #

Makeable GroupName Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m GroupName Source #

Makeable JannoAlternativeID Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoCaptureType Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoCollectionID Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoComment Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoComment Source #

Makeable JannoContamination Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoContaminationErr Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoContaminationMeas Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoContaminationNote Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoCountry Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoCountry Source #

Makeable JannoCountryISO Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoCoverageOnTargets Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDamage Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoDamage Source #

Makeable JannoDataPreparationPipelineURL Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateBCADMedian Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateBCADStart Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateBCADStop Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateC14Labnr Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateC14UncalBP Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateC14UncalBPErr Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoDateNote Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoDateNote Source #

Makeable JannoDateType Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoDateType Source #

Makeable JannoEndogenous Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoGeneticSourceAccessionID Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoGenotypePloidy Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoKeyword Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoKeyword Source #

Makeable JannoLatitude Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoLatitude Source #

Makeable JannoLibraryBuilt Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoLibraryName Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoLocation Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoLocation Source #

Makeable JannoLongitude Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoMTHaplogroup Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoNrLibraries Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoNrSNPs Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoNrSNPs Source #

Makeable JannoPrimaryContact Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoPublication Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoRelationDegree Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoRelationNote Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoRelationTo Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoRelationType Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoSite Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoSite Source #

Makeable JannoSourceTissue Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable JannoUDG Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Methods

make :: MonadFail m => Text -> m JannoUDG Source #

Makeable JannoYHaplogroup Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Makeable SSFAccessionIDRun Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFAccessionIDSample Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFAccessionIDStudy Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFFastqASPERAURI Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFFastqBytes Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Methods

make :: MonadFail m => Text -> m SSFFastqBytes Source #

Makeable SSFFastqFTPURI Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFFastqMD5 Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Methods

make :: MonadFail m => Text -> m SSFFastqMD5 Source #

Makeable SSFFirstPublicSimpleDate Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFInstrumentModel Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFInstrumentPlatform Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFLastUpdatedSimpleDate Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFLibraryBuilt Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFLibraryLayout Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFLibraryName Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFLibrarySource Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFLibraryStrategy Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFReadCount Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Methods

make :: MonadFail m => Text -> m SSFReadCount Source #

Makeable SSFSampleAlias Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFSecondarySampleAccession Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFSubmittedFTPURI Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Makeable SSFUDG Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Methods

make :: MonadFail m => Text -> m SSFUDG Source #

class Suspicious a where Source #

Methods

inspect :: a -> Maybe [String] Source #

Instances

Instances details
Suspicious GeneticSex Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious GroupName Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoAlternativeID Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoCaptureType Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoCollectionID Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoComment Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoContamination Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoContaminationErr Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoContaminationMeas Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoContaminationNote Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoCountry Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoCountryISO Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoCoverageOnTargets Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDamage Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDataPreparationPipelineURL Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateBCADMedian Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateBCADStart Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateBCADStop Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateC14Labnr Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateC14UncalBP Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateC14UncalBPErr Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateNote Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoDateType Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoEndogenous Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoGeneticSourceAccessionID Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoGenotypePloidy Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoKeyword Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoLatitude Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoLibraryBuilt Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoLibraryName Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoLocation Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoLongitude Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoMTHaplogroup Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoNrLibraries Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoNrSNPs Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoPrimaryContact Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoPublication Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoRelationDegree Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoRelationNote Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoRelationTo Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoRelationType Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoSite Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoSourceTissue Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoUDG Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious JannoYHaplogroup Source # 
Instance details

Defined in Poseidon.ColumnTypesJanno

Suspicious SSFAccessionIDRun Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFAccessionIDSample Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFAccessionIDStudy Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFFastqASPERAURI Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFFastqBytes Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFFastqFTPURI Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFFastqMD5 Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFFirstPublicSimpleDate Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFInstrumentModel Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFInstrumentPlatform Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFLastUpdatedSimpleDate Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFLibraryBuilt Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFLibraryLayout Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFLibraryName Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFLibrarySource Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFLibraryStrategy Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFReadCount Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFSampleAlias Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFSecondarySampleAccession Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFSubmittedFTPURI Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious SSFUDG Source # 
Instance details

Defined in Poseidon.ColumnTypesSSF

Suspicious CsvNamedRecord Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Suspicious String Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Suspicious a => Suspicious (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Suspicious a => Suspicious (Maybe a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Methods

inspect :: Maybe a -> Maybe [String] Source #

inspectEachField :: (Generic a, Code a ~ '[xs], All Suspicious xs) => a -> [Maybe [String]] Source #

parseTypeCSV :: forall a m. (MonadFail m, Makeable a, Typeable a) => String -> ByteString -> m a Source #

decodingOptions :: DecodeOptions Source #

encodingOptions :: EncodeOptions Source #

newtype CsvNamedRecord Source #

A datatype to collect additional, unpecified .csv.tsv file columns (a hashmap in cassavaData.Csv)

Constructors

CsvNamedRecord NamedRecord 

Instances

Instances details
Generic CsvNamedRecord Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Associated Types

type Rep CsvNamedRecord :: Type -> Type #

Show CsvNamedRecord Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Eq CsvNamedRecord Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

PresenceCountable CsvNamedRecord Source # 
Instance details

Defined in Poseidon.CLI.Survey

Suspicious CsvNamedRecord Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

type Rep CsvNamedRecord Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

type Rep CsvNamedRecord = D1 ('MetaData "CsvNamedRecord" "Poseidon.ColumnTypesUtils" "poseidon-hs-1.6.7.3-GB1MYUceETwBAiXCnu0Oii" 'True) (C1 ('MetaCons "CsvNamedRecord" 'PrefixI 'False) (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 NamedRecord)))

getCsvNR :: CsvNamedRecord -> NamedRecord Source #

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

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

explicitNA :: NamedRecord -> NamedRecord Source #

newtype ListColumn a Source #

A general datatype for janno list columns

Constructors

ListColumn 

Fields

Instances

Instances details
Generic (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

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.ColumnTypesUtils

FromField a => FromField (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Methods

parseField :: Field -> Parser (ListColumn a)

(ToField a, Show a) => ToField (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Methods

toField :: ListColumn a -> Field

Eq a => Eq (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

Methods

(==) :: ListColumn a -> ListColumn a -> Bool #

(/=) :: ListColumn a -> ListColumn a -> Bool #

Ord a => Ord (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

PresenceCountable (ListColumn a) Source # 
Instance details

Defined in Poseidon.CLI.Survey

Suspicious a => Suspicious (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

type Rep (ListColumn a) Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils

type Rep (ListColumn a) = D1 ('MetaData "ListColumn" "Poseidon.ColumnTypesUtils" "poseidon-hs-1.6.7.3-GB1MYUceETwBAiXCnu0Oii" 'True) (C1 ('MetaCons "ListColumn" 'PrefixI 'True) (S1 ('MetaSel ('Just "getListColumn") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [a])))

data CsvParseError Source #

Constructors

CsvParseError 

Instances

Instances details
Show CsvParseError Source # 
Instance details

Defined in Poseidon.ColumnTypesUtils