{-# LANGUAGE DeriveGeneric #-}
module SLynx.Concatenate.Options
( ConcatenateArguments (..),
concatenateArguments,
)
where
import Control.Applicative
import ELynx.Data.Alphabet.Alphabet
import ELynx.Tools
import Options.Applicative
import SLynx.Tools
data ConcatenateArguments = ConcatenateArguments
{ ccAlphabet :: Alphabet,
ccInFiles :: [FilePath]
}
deriving (Eq, Show, Generic)
instance Reproducible ConcatenateArguments where
inFiles = ccInFiles
outSuffixes _ = [".fasta"]
getSeed _ = Nothing
setSeed = const
parser = concatenateArguments
cmdName = "concatenate"
cmdDsc = ["Concatenate sequences found in input files."]
instance FromJSON ConcatenateArguments
instance ToJSON ConcatenateArguments
concatenateArguments :: Parser ConcatenateArguments
concatenateArguments = ConcatenateArguments <$> alphabetOpt <*> some inFileArg
inFileArg :: Parser FilePath
inFileArg =
strArgument $ metavar "INPUT-FILE" <> help "Read sequences from INPUT-FILE"