| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
SequenceTools.PileupCaller
Synopsis
- callToDosage :: Char -> Char -> Call -> Maybe (Int, Int)
- data Call
- callGenotypeFromPileup :: CallingMode -> Int -> String -> IO Call
- callMajorityAllele :: Bool -> Int -> String -> IO Call
- findMajorityAlleles :: String -> [Char]
- callRandomAllele :: String -> IO Call
- callRandomDiploid :: String -> IO Call
- data CallingMode
- data TransitionsMode
- filterTransitions :: forall (m :: Type -> Type). Monad m => TransitionsMode -> Pipe (Maybe PileupRow, FreqSumEntry) (Maybe PileupRow, FreqSumEntry) m ()
- cleanSSdamageAllSamples :: Char -> Char -> [String] -> [[Strand]] -> [String]
- computeAlleleFreq :: [Maybe (Int, Int)] -> Maybe Double
Documentation
callToDosage :: Char -> Char -> Call -> Maybe (Int, Int) Source #
a function to turn a call into the dosage of non-reference alleles
A datatype to represent a single genotype call
Constructors
| HaploidCall Char | |
| DiploidCall Char Char | |
| MissingCall |
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)
data CallingMode Source #
A datatype to specify the calling mode
Constructors
| MajorityCalling Bool | |
| RandomCalling | |
| RandomDiploidCalling |
Instances
| Show CallingMode Source # | |
Defined in SequenceTools.PileupCaller Methods showsPrec :: Int -> CallingMode -> ShowS # show :: CallingMode -> String # showList :: [CallingMode] -> ShowS # | |
data TransitionsMode Source #
Constructors
| TransitionsMissing | |
| SkipTransitions | |
| SingleStrandMode | |
| AllSites |
Instances
| Show TransitionsMode Source # | |
Defined in SequenceTools.PileupCaller Methods showsPrec :: Int -> TransitionsMode -> ShowS # show :: TransitionsMode -> String # showList :: [TransitionsMode] -> ShowS # | |
| Eq TransitionsMode Source # | |
Defined in SequenceTools.PileupCaller Methods (==) :: TransitionsMode -> TransitionsMode -> Bool # (/=) :: TransitionsMode -> TransitionsMode -> Bool # | |
filterTransitions :: forall (m :: Type -> Type). Monad m => TransitionsMode -> Pipe (Maybe PileupRow, FreqSumEntry) (Maybe PileupRow, FreqSumEntry) m () Source #