{-# LANGUAGE DeriveGeneric #-}
module SLynx.Examine.Options
( ExamineArguments (..),
examineArguments,
)
where
import ELynx.Data.Alphabet.Alphabet
import ELynx.Tools
import Options.Applicative
import SLynx.Tools
data ExamineArguments = ExamineArguments
{ exAlphabet :: Alphabet,
exInFile :: FilePath,
exPerSite :: Bool
}
deriving (Eq, Show, Generic)
instance Reproducible ExamineArguments where
inFiles = pure . exInFile
outSuffixes _ = [".out"]
getSeed _ = Nothing
setSeed = const
parser = examineArguments
cmdName = "examine"
cmdDsc =
[ "Examine sequences. If data is a multi sequence alignment, additionally analyze columns."
]
instance FromJSON ExamineArguments
instance ToJSON ExamineArguments
examineArguments :: Parser ExamineArguments
examineArguments =
ExamineArguments <$> alphabetOpt <*> filePathArg <*> examinePerSiteOpt
examinePerSiteOpt :: Parser Bool
examinePerSiteOpt =
switch $ long "per-site" <> help "Report per site summary statistics"
filePathArg :: Parser FilePath
filePathArg =
strArgument $ metavar "INPUT-FILE" <> help "Read sequences from INPUT-FILE"