From ed98174bbefc85f9895c870fdb7518e2a534a150 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 28 Jul 2021 08:07:32 +1000
Subject: bugfix: use unsorted type for alignment output

Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
---
 tools/snap-align.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tools/snap-align.nix')

diff --git a/tools/snap-align.nix b/tools/snap-align.nix
index 4647142..279cf20 100644
--- a/tools/snap-align.nix
+++ b/tools/snap-align.nix
@@ -32,6 +32,6 @@ in stage {
       ${optionalString (flags != null) flags} \
       | samtools sort -n > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
-- 
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