Genomic.hs

module SequenceFormats.Genomic where

import SequenceFormats.Bed (BedEntry(..), filterThroughBed)
import SequenceFormats.Eigenstrat (EigenstratSnpEntry(..))
import SequenceFormats.FreqSum (FreqSumEntry(..))
import SequenceFormats.Pileup (PileupRow(..))
import SequenceFormats.Utils (Chrom)
import SequenceFormats.VCF (VCFentry(..))

import Pipes (Producer)

class Genomic a where
    genomicPosition :: a -> (Chrom, Int)

    genomicChrom :: a -> Chrom
    genomicChrom = fst . genomicPosition

    genomicBase :: a -> Int 
    genomicBase = snd . genomicPosition

instance Genomic EigenstratSnpEntry where
    genomicPosition (EigenstratSnpEntry c p _ _ _ _) = (c, p)

instance Genomic FreqSumEntry where
    genomicPosition (FreqSumEntry c p _ _ _ _ _) = (c, p)

instance Genomic PileupRow where
    genomicPosition (PileupRow c p _ _ _) = (c, p)

instance Genomic VCFentry where
    genomicPosition (VCFentry c p _ _ _ _ _ _ _ _) = (c, p)

chromFilter :: (Genomic e) => [Chrom] -> e -> Bool
chromFilter exclusionList = (`notElem` exclusionList) . genomicChrom

genomicFilterThroughBed :: (Monad m, Genomic e) => Producer BedEntry m () -> Producer e m () -> Producer e m ()
genomicFilterThroughBed bedProd = filterThroughBed bedProd genomicPosition