From c2da3532235bd45ddb1105600d4ba74a70dadeca Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 15 Nov 2018 15:13:50 +1100
Subject: gridss.softClipsToSplitReads: sort ordering is not preserved

NB: this breaks gridss.preprocessBam
---
 tools/gridss-softClipsToSplitReads.nix | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

(limited to 'tools')

diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index b35d41d..5fce894 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -37,9 +37,5 @@ stdenv.mkDerivation rec {
       ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
-  passthru.filetype =
-    if alignerStreaming then
-      filetype.bam { ref = ref; sort = sorting.none {};  }
-    else
-      input.filetype;
+  passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {};  }
 }
-- 
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