SequenceTools.PileupCaller

Documentation

callToDosage :: Char -> Char -> Call -> Maybe Int

a function to turn a call into the dosage of non-reference alleles

data Call

A datatype to represent a single genotype call

Constructors

HaploidCall Char

DiploidCall Char Char

MissingCall

Instances

Eq Call

Defined in SequenceTools.PileupCaller

Methods

(==) :: Call -> Call -> Bool

(/=) :: Call -> Call -> Bool

Show Call

Defined in SequenceTools.PileupCaller

Methods

showsPrec :: Int -> Call -> ShowS

show :: Call -> String

showList :: [Call] -> ShowS

callGenotypeFromPileup :: CallingMode -> Int -> String -> IO Call

Make a call from alleles

callMajorityAllele :: Bool -> Int -> String -> IO Call

Sample the majority allele, or one of the majority alleles

findMajorityAlleles :: String -> [Char]

Find the majority allele(s)

callRandomAllele :: String -> IO Call

call a random allele

callRandomDiploid :: String -> IO Call

call two random alleles

dosageToEigenstratGeno :: Bool -> Maybe Int -> GenoEntry

convert a Dosage to an eigenstrat-encoded genotype

freqSumToEigenstrat :: Bool -> FreqSumEntry -> (EigenstratSnpEntry, GenoLine)

convert a freqSum entry to an eigenstrat SNP entry

data CallingMode

A datatype to specify the calling mode

Constructors

MajorityCalling Bool

RandomCalling

RandomDiploidCalling

data TransitionsMode

Constructors

TransitionsMissing

SkipTransitions

SingleStrandMode

AllSites

Instances

Eq TransitionsMode

Defined in SequenceTools.PileupCaller

Methods

(==) :: TransitionsMode -> TransitionsMode -> Bool

(/=) :: TransitionsMode -> TransitionsMode -> Bool

filterTransitions :: Monad m => TransitionsMode -> Pipe FreqSumEntry FreqSumEntry m ()

cleanSSdamageAllSamples :: Char -> Char -> [String] -> [[Strand]] -> [String]