| Safe Haskell | Safe-Inferred |
|---|---|
| Language | Haskell2010 |
Poseidon.CLI.Forge
Synopsis
- data ForgeOptions = ForgeOptions {
- _forgeGenoSources :: [GenoDataSource]
- _forgeEntityInput :: [EntityInput SignedEntity]
- _forgeSnpFile :: Maybe FilePath
- _forgeIntersect :: Bool
- _forgeOutFormat :: GenotypeFormatSpec
- _forgeOutMode :: ForgeOutMode
- _forgeOutPacPath :: FilePath
- _forgeOutPacName :: Maybe String
- _forgePackageWise :: Bool
- _forgeOutputPlinkPopMode :: PlinkPopNameMode
- _forgeOutputOrdered :: Bool
- data ForgeOutMode
- preservePyml :: ForgeOutMode -> Bool
- pacReadOpts :: PackageReadOptions
- runForge :: ForgeOptions -> PoseidonIO ()
- sumNonMissingSNPs :: IOVector Int -> (EigenstratSnpEntry, GenoLine) -> SafeT IO (IOVector Int)
- filterSeqSourceRows :: JannoRows -> SeqSourceRows -> SeqSourceRows
- filterBibEntries :: JannoRows -> BibTeX -> BibTeX
- fillMissingSnpSets :: [PoseidonPackage] -> PoseidonIO [SNPSetSpec]
Documentation
data ForgeOptions Source #
A datatype representing command line options for the survey command
Constructors
data ForgeOutMode Source #
Different output modes ordered from more minimal to more complete
Constructors
| GenoOut | |
| MinimalOut | |
| PreservePymlOut | |
| NormalOut |
preservePyml :: ForgeOutMode -> Bool Source #
runForge :: ForgeOptions -> PoseidonIO () Source #
The main function running the forge command
sumNonMissingSNPs :: IOVector Int -> (EigenstratSnpEntry, GenoLine) -> SafeT IO (IOVector Int) Source #
fillMissingSnpSets :: [PoseidonPackage] -> PoseidonIO [SNPSetSpec] Source #