sequenceTools-1.4.0.5: A package with tools for processing DNA sequencing data

Safe HaskellNone
LanguageHaskell2010

SequenceTools.PileupCaller

Synopsis

Documentation

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

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

data Call Source #

A datatype to represent a single genotype call

Instances
Eq Call Source # 
Instance details

Defined in SequenceTools.PileupCaller

Methods

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

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

Show Call Source # 
Instance details

Defined in SequenceTools.PileupCaller

Methods

showsPrec :: Int -> Call -> ShowS #

show :: Call -> String #

showList :: [Call] -> ShowS #

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

Make a call from alleles

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

Sample the majority allele, or one of the majority alleles

findMajorityAlleles :: String -> [Char] Source #

Find the majority allele(s)

callRandomAllele :: String -> IO Call Source #

call a random allele

callRandomDiploid :: String -> IO Call Source #

call two random alleles

data CallingMode Source #

A datatype to specify the calling mode