From 8fb986fd88705fc01be7145b04fa229092c1e69e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 29 Oct 2018 15:32:50 +1100
Subject: bwa-mem: BWA output is query name sorted

---
 tools/bwa-mem.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index eed488e..3420294 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -36,5 +36,5 @@ in stdenv.mkDerivation {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.none {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
 }
-- 
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