From 7c29ef494f974b457bfef6a5af7d37fa03bb7952 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 29 Jul 2021 16:19:30 +1000
Subject: initial import

---
 xenomapper.hs | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 xenomapper.hs

(limited to 'xenomapper.hs')

diff --git a/xenomapper.hs b/xenomapper.hs
new file mode 100644
index 0000000..123b1a5
--- /dev/null
+++ b/xenomapper.hs
@@ -0,0 +1,41 @@
+{-# 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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