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

---
 biohazard.patch | 13 +++++++++++++
 default.nix     | 21 +++++++++++++++++++++
 shell.nix       | 12 ++++++++++++
 xenomapper.hs   | 41 +++++++++++++++++++++++++++++++++++++++++
 4 files changed, 87 insertions(+)
 create mode 100644 biohazard.patch
 create mode 100644 default.nix
 create mode 100644 shell.nix
 create mode 100644 xenomapper.hs

diff --git a/biohazard.patch b/biohazard.patch
new file mode 100644
index 0000000..b075312
--- /dev/null
+++ b/biohazard.patch
@@ -0,0 +1,13 @@
+diff --git a/Control/Monad/Log.hs b/Control/Monad/Log.hs
+index 5b6598a..de4589f 100644
+--- a/Control/Monad/Log.hs
++++ b/Control/Monad/Log.hs
+@@ -14,7 +14,7 @@ module Control.Monad.Log
+     , panic
+     ) where
+ 
+-import BasePrelude           hiding ( try, catchIOError )
++import BasePrelude           hiding ( try, catchIOError, option )
+ import Control.Monad.Base           ( MonadBase(..) )
+ import Control.Monad.Catch
+ import Control.Monad.Primitive
diff --git a/default.nix b/default.nix
new file mode 100644
index 0000000..3314d66
--- /dev/null
+++ b/default.nix
@@ -0,0 +1,21 @@
+let
+  pkgs = import <nixpkgs> { };
+
+  ghc = with pkgs.haskell.lib;
+    pkgs.ghc.withPackages (pkgs:
+      with pkgs;
+      [
+        (doJailbreak (markUnbroken
+          (biohazard.overrideAttrs (_: { patches = [ ./biohazard.patch ]; }))))
+      ]);
+in pkgs.stdenv.mkDerivation {
+  name = "xenomapper-hs";
+  buildInputs = [ ghc ];
+  src = ./.;
+  buildPhase = ''
+    ghc -O3 xenomapper.hs -o xenomapper
+  '';
+  installPhase = ''
+    install -D xenomapper $out/bin/xenomapper
+  '';
+}
diff --git a/shell.nix b/shell.nix
new file mode 100644
index 0000000..40ee189
--- /dev/null
+++ b/shell.nix
@@ -0,0 +1,12 @@
+let
+  pkgs = import <nixpkgs> { };
+
+  ghc = with pkgs.haskell.lib;
+    pkgs.ghc.withPackages (pkgs:
+      with pkgs;
+      [
+        hlint
+        (doJailbreak (markUnbroken
+          (biohazard.overrideAttrs (_: { patches = [ ./biohazard.patch ]; }))))
+      ]);
+in pkgs.mkShell { buildInputs = [ ghc ]; }
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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