poseidon-hs-1.6.0.0: A package with tools for working with Poseidon genotype data
Safe HaskellSafe-Inferred
LanguageHaskell2010

Poseidon.CLI.Jannocoalesce

Documentation

data JannoSourceSpec Source #

Constructors

JannoSourceSingle FilePath 
JannoSourceBaseDirs [FilePath] 

data CoalesceJannoColumnSpec Source #

Constructors

AllJannoColumns 
IncludeJannoColumns [ByteString] 
ExcludeJannoColumns [ByteString] 

data JannoCoalesceOptions Source #

Constructors

JannoCoalesceOptions 

Fields

runJannocoalesce :: JannoCoalesceOptions -> PoseidonIO () Source #

type CounterMismatches = IORef Int Source #

type CounterCopied = IORef Int Source #

makeNewJannoRows :: [JannoRow] -> [JannoRow] -> CoalesceJannoColumnSpec -> Bool -> String -> String -> Maybe String -> PoseidonIO [JannoRow] Source #

getKeyFromJanno :: MonadThrow m => JannoRow -> String -> m String Source #

matchWithOptionalStrip :: Maybe String -> String -> String -> Bool Source #

mergeRow :: CounterCopied -> JannoRow -> JannoRow -> CoalesceJannoColumnSpec -> Bool -> String -> String -> PoseidonIO JannoRow Source #