| 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
- writeJannoFile :: FilePath -> JannoRows -> IO ()
- writeJannoFileWithoutEmptyCols :: FilePath -> JannoRows -> IO ()
- readJannoFile :: FilePath -> PoseidonIO JannoRows
- createMinimalJanno :: [EigenstratIndEntry] -> JannoRows
- createMinimalSample :: EigenstratIndEntry -> JannoRow
- jannoHeaderString :: [String]
- newtype JannoRows = JannoRows {
- getJannoRows :: [JannoRow]
- jannoRows2EigenstratIndEntries :: JannoRows -> [EigenstratIndEntry]
- makeHeaderWithAdditionalColumns :: [JannoRow] -> Header
Documentation
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
Instances
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 #
A data type to represent a janno file
Constructors
| JannoRows | |
Fields
| |
jannoRows2EigenstratIndEntries :: JannoRows -> [EigenstratIndEntry] Source #
a convenience function to construct Eigenstrat Ind entries out of jannoRows
makeHeaderWithAdditionalColumns :: [JannoRow] -> Header Source #