Types

Documentation

data Preprocess

Constructors

Assembly

NonAssembly Char

Instances

Read Preprocess

Defined in Types

Methods

readsPrec :: Int -> ReadS Preprocess

readList :: ReadS [Preprocess]

readPrec :: ReadPrec Preprocess

readListPrec :: ReadPrec [Preprocess]

Show Preprocess

Defined in Types

Methods

showsPrec :: Int -> Preprocess -> ShowS

show :: Preprocess -> String

showList :: [Preprocess] -> ShowS

data TrinityArgs

Constructors

TrinityBase

TrinityGenome

TrinityCustom String

Instances

Read TrinityArgs

Defined in Types

Methods

readsPrec :: Int -> ReadS TrinityArgs

readList :: ReadS [TrinityArgs]

readPrec :: ReadPrec TrinityArgs

readListPrec :: ReadPrec [TrinityArgs]

Show TrinityArgs

Defined in Types

Methods

showsPrec :: Int -> TrinityArgs -> ShowS

show :: TrinityArgs -> String

showList :: [TrinityArgs] -> ShowS

data Query

Constructors

QueryFile FilePath

QueryShell (Shell Line)

newtype Position

Constructors

Position

Fields

• unPosition :: Int

Instances

Show Position

Defined in Types

Methods

showsPrec :: Int -> Position -> ShowS

show :: Position -> String

showList :: [Position] -> ShowS

newtype Sequence

Constructors

Sequence

Fields

• unSequence :: Text

Instances

Show Sequence

Defined in Types

Methods

showsPrec :: Int -> Sequence -> ShowS

show :: Sequence -> String

showList :: [Sequence] -> ShowS

newtype Fill

Constructors

Fill

Fields

• unFill :: Char

Instances

Show Fill

Defined in Types

Methods

showsPrec :: Int -> Fill -> ShowS

show :: Fill -> String

showList :: [Fill] -> ShowS

newtype Command

Constructors

Command

Fields

• unCommand :: Text

Instances

Show Command

Defined in Types

Methods

showsPrec :: Int -> Command -> ShowS

show :: Command -> String

showList :: [Command] -> ShowS

newtype Args

Constructors

Args

Fields

• unArgs :: String

Instances

Show Args

Defined in Types

Methods

showsPrec :: Int -> Args -> ShowS

show :: Args -> String

showList :: [Args] -> ShowS

newtype Subject

Constructors

Subject

Fields

• unSubject :: FilePath

Instances

Show Subject

Defined in Types

Methods

showsPrec :: Int -> Subject -> ShowS

show :: Subject -> String

showList :: [Subject] -> ShowS

newtype BamRow

Constructors

BamRow

Fields

• unBamRow :: [Text]

Instances

Read BamRow

Defined in Types

Methods

readsPrec :: Int -> ReadS BamRow

readList :: ReadS [BamRow]

readPrec :: ReadPrec BamRow

readListPrec :: ReadPrec [BamRow]

Show BamRow

Defined in Types

Methods

showsPrec :: Int -> BamRow -> ShowS

show :: BamRow -> String

showList :: [BamRow] -> ShowS

newtype Headers

Constructors

Headers

Fields

• unHeaders :: Text

newtype AbundanceMap

Constructors

AbundanceMap

Fields

• unAbundanceMap :: Map Text Double

newtype FrequencyMap

Constructors

FrequencyMap

Fields

• unFrequencyMap :: Map Text Double

newtype DuplicationRow

Constructors

DuplicationRow

Fields

• unDuplicationRow :: Map Text Text

newtype PositionMap

Constructors

PositionMap

Fields

• unPositionMap :: IntMap Char

newtype AccessionMap

Constructors

AccessionMap

Fields

• unAccessionMap :: Map Text Text

Instances

Read AccessionMap

Defined in Types

Methods

readsPrec :: Int -> ReadS AccessionMap

readList :: ReadS [AccessionMap]

readPrec :: ReadPrec AccessionMap

readListPrec :: ReadPrec [AccessionMap]

Show AccessionMap

Defined in Types

Methods

showsPrec :: Int -> AccessionMap -> ShowS

show :: AccessionMap -> String

showList :: [AccessionMap] -> ShowS

newtype BlastSet

Constructors

BlastSet

Fields

• unBlastSet :: Set Text

newtype AccSet

Constructors

AccSet

Fields

• unAccSet :: Set Text

newtype MatchMap

Constructors

MatchMap

Fields

• unMatchMap :: Map Text Bool