blob: 3317a53509c94b48cd957d501179541c87eef064 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
{-# LANGUAGE DataKinds #-}
{-# LANGUAGE DeriveGeneric #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE LambdaCase #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE StandaloneDeriving #-}
{-# LANGUAGE TypeApplications #-}
{-# LANGUAGE TypeFamilies #-}
{-# LANGUAGE TypeOperators #-}
{-# OPTIONS_GHC -Wno-orphans #-}
module Main where
import Data.ByteString (ByteString)
import qualified Data.ByteString as B
import Data.Cuckoo
import Data.FastQ
import Data.Function
import GHC.Prim (RealWorld)
import GHC.TypeLits
import Lens.Micro
import Options.Generic
import qualified Streamly.Data.Stream as S
newtype NoLabel a = NoLabel {unNoLabel :: a} deriving (Generic)
data Options w = Options
{ umiLength :: w ::: Natural <?> "length of UMI prefix" <!> "8",
extraHashBases :: w ::: Natural <?> "extra hash bases to use for location proxy" <!> "4",
filterSize :: w ::: Natural <?> "Cuckoo filter size" <!> "200000000",
input1 :: w ::: NoLabel FilePath <?> "input fastq 1 path",
input2 :: w ::: NoLabel FilePath <?> "input fastq 2 path",
output1 :: w ::: NoLabel FilePath <?> "output fastq 1 path",
output2 :: w ::: NoLabel FilePath <?> "output fastq 2 path"
}
deriving (Generic)
instance ParseFields a => ParseRecord (NoLabel a)
instance ParseFields a => ParseFields (NoLabel a) where
parseFields msg _ _ def = fmap NoLabel (parseFields msg Nothing Nothing def)
instance ParseRecord (Options Wrapped)
instance CuckooFilterHash ByteString where
cuckooHash (Salt s) = saltedFnv1aByteString s
cuckooFingerprint (Salt s) = saltedSipHashByteString s
{-# INLINE cuckooHash #-}
{-# INLINE cuckooFingerprint #-}
trim :: Int -> ReadPair -> ReadPair
trim sz x =
x
& _1 . nucs %~ B.drop sz
& _2 . nucs %~ B.drop sz
& _1 . qual %~ B.drop sz
& _2 . qual %~ B.drop sz
insert' :: (KnownNat b, KnownNat f) => Int -> CuckooFilter RealWorld b f ByteString -> ReadPair -> IO Bool
insert' sz f x =
let y = B.take sz (x ^. _1 . nucs) <> B.take sz (x ^. _2 . nucs)
in member f y >>= \case
True -> pure False
False ->
insert f y >>= \case
True -> pure True
False -> error "filter full"
main :: IO ()
main = do
opts <- unwrapRecord "UMI deduplication"
f <- newCuckooFilter @4 @13 @ByteString 0 (filterSize opts)
parse (unNoLabel $ input1 opts) (unNoLabel $ input2 opts)
& S.filterM (insert' (fromIntegral $ umiLength opts + extraHashBases opts) f)
& fmap (trim . fromIntegral $ umiLength opts)
& unparse (unNoLabel $ output1 opts) (unNoLabel $ output2 opts)
|
