Safe Haskell	None
Language	Haskell2010

SequenceFormats.FreqSum

Description

Module to parse and write freqSum files. The freqsum format is defined here: https://rarecoal-docs.readthedocs.io/en/latest/rarecoal-tools.html#vcf2freqsum

Synopsis

readFreqSumStdIn :: (MonadIO m, MonadThrow m) => m (FreqSumHeader, Producer FreqSumEntry m ())
readFreqSumFile :: MonadSafe m => FilePath -> m (FreqSumHeader, Producer FreqSumEntry m ())
data FreqSumEntry = FreqSumEntry {
- fsChrom :: Chrom
- fsPos :: Int
- fsSnpId :: Maybe ByteString
- fsGeneticPos :: Maybe Double
- fsRef :: Char
- fsAlt :: Char
- fsCounts :: [Maybe Int]
}
data FreqSumHeader = FreqSumHeader {
- fshNames :: [String]
- fshCounts :: [Int]
}
printFreqSumStdOut :: MonadIO m => FreqSumHeader -> Consumer FreqSumEntry m ()
printFreqSumFile :: MonadSafe m => FilePath -> FreqSumHeader -> Consumer FreqSumEntry m ()
freqSumEntryToText :: FreqSumEntry -> ByteString

Documentation

readFreqSumStdIn :: (MonadIO m, MonadThrow m) => m (FreqSumHeader, Producer FreqSumEntry m ()) Source #

A function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.

readFreqSumFile :: MonadSafe m => FilePath -> m (FreqSumHeader, Producer FreqSumEntry m ()) Source #

A function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.

data FreqSumEntry Source #

A Datatype to denote a single freqSum line

Constructors

FreqSumEntry

Fields

fsChrom :: Chrom
The chromosome of the site
fsPos :: Int
The position of the site
fsSnpId :: Maybe ByteString
An optional parameter to take the snpId. This is not parsed from or printed to freqSum format but is used in internal conversions from Eigenstrat.
fsGeneticPos :: Maybe Double
An optional parameter to take the genetic pos. This is not parsed from or printed to freqSum format but is used in internal conversions from Eigenstrat.
fsRef :: Char
The reference allele
fsAlt :: Char
The alternative allele
fsCounts :: [Maybe Int]
A list of allele counts in each group. Nothing denotes missing data.

Instances

Eq FreqSumEntry Source #
Instance details Defined in SequenceFormats.FreqSum Methods (==) :: FreqSumEntry -> FreqSumEntry -> Bool # (/=) :: FreqSumEntry -> FreqSumEntry -> Bool #
Show FreqSumEntry Source #
Instance details Defined in SequenceFormats.FreqSum Methods showsPrec :: Int -> FreqSumEntry -> ShowS # show :: FreqSumEntry -> String # showList :: [FreqSumEntry] -> ShowS #

data FreqSumHeader Source #

A Datatype representing the Header

Constructors

FreqSumHeader
Fields fshNames :: [String] A list of individual or group names fshCounts :: [Int] A list of haplotype counts per individual/group.

Instances

Eq FreqSumHeader Source #
Instance details Defined in SequenceFormats.FreqSum Methods (==) :: FreqSumHeader -> FreqSumHeader -> Bool # (/=) :: FreqSumHeader -> FreqSumHeader -> Bool #
Show FreqSumHeader Source #
Instance details Defined in SequenceFormats.FreqSum Methods showsPrec :: Int -> FreqSumHeader -> ShowS # show :: FreqSumHeader -> String # showList :: [FreqSumHeader] -> ShowS #

printFreqSumStdOut :: MonadIO m => FreqSumHeader -> Consumer FreqSumEntry m () Source #

A function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.

printFreqSumFile :: MonadSafe m => FilePath -> FreqSumHeader -> Consumer FreqSumEntry m () Source #

A function that writes a freqSum file. Expects the FilePath and the freqSum header as arguments, and then returns a Consumer that accepts freqSum entries.

freqSumEntryToText :: FreqSumEntry -> ByteString Source #

This function converts a single freqSum entry to a printable freqSum line.