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{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE ViewPatterns #-}
module Main where
import Bio.Prelude hiding ((.))
import Bio.Bam
import Control.Monad
import Control.Monad.Log
import Control.Monad.IO.Class
import System.Environment
import qualified Streaming.Prelude as S
import Streaming.Prelude (Stream, Of)
filterBams :: (MonadIO m, MonadLog m, MonadMask m) => Stream (Of BamRaw) m () -> Stream (Of BamRaw) m () -> Stream (Of BamRaw) m ()
filterBams a b = do
str0 <- lift $ S.next a
str1 <- lift $ S.next b
loop str0 str1
where
loop a@(Right (a', a'')) b@(Right (b', b'')) =
case compare (qname a') (qname b') of
EQ -> do
when (as a' > as b') $ S.yield a'
filterBams a'' b''
LT -> do
n <- lift $ S.next a''
loop n b
GT -> do
n <- lift $ S.next b''
loop a n
loop _ _ = return ()
qname = b_qname . unpackBam
as = extAsInt 0 "AS" . unpackBam
main = do
args <- getArgs
withLogging_ (LoggingConf Warning Error Error 10 True) $ do
decodeBamFiles args (\[(hdr, prim), (_, sec)] -> writeBamFile "primary.bam" hdr $ filterBams prim sec)
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