-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | A package with tools for processing next generation sequencing data, in particular for processing data from ancient DNA sequencing libraries.
--   
--   Key tool in this package is pileupCaller, a tool to randomly sample
--   genotypes from sequencing data.
@package sequenceTools
@version 1.4.0.1

module SequenceTools.Utils
versionInfoOpt :: Parser (a -> a)
versionInfoText :: String
sampleWithoutReplacement :: [a] -> Int -> IO (Maybe [a])

module SequenceTools.PileupCaller

-- | a function to turn a call into the dosage of non-reference alleles
callToDosage :: Char -> Char -> Call -> Maybe Int

-- | A datatype to represent a single genotype call
data Call
HaploidCall :: Char -> Call
DiploidCall :: Char -> Char -> Call
MissingCall :: Call

-- | Make a call from alleles
callGenotypeFromPileup :: CallingMode -> Int -> String -> IO Call

-- | Sample the majority allele, or one of the majority alleles
callMajorityAllele :: Bool -> Int -> String -> IO Call

-- | Find the majority allele(s)
findMajorityAlleles :: String -> [Char]

-- | call a random allele
callRandomAllele :: String -> IO Call

-- | call two random alleles
callRandomDiploid :: String -> IO Call

-- | convert a Dosage to an eigenstrat-encoded genotype
dosageToEigenstratGeno :: Bool -> Maybe Int -> GenoEntry

-- | convert a freqSum entry to an eigenstrat SNP entry
freqSumToEigenstrat :: Bool -> FreqSumEntry -> (EigenstratSnpEntry, GenoLine)

-- | A datatype to specify the calling mode
data CallingMode
MajorityCalling :: Bool -> CallingMode
RandomCalling :: CallingMode
RandomDiploidCalling :: CallingMode
data TransitionsMode
TransitionsMissing :: TransitionsMode
SkipTransitions :: TransitionsMode
SingleStrandMode :: TransitionsMode
AllSites :: TransitionsMode
filterTransitions :: Monad m => TransitionsMode -> Pipe FreqSumEntry FreqSumEntry m ()
cleanSSdamageAllSamples :: Char -> Char -> [String] -> [[Strand]] -> [String]
instance GHC.Classes.Eq SequenceTools.PileupCaller.TransitionsMode
instance GHC.Classes.Eq SequenceTools.PileupCaller.Call
instance GHC.Show.Show SequenceTools.PileupCaller.Call