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).
---
 examples/call.nix             | 1 +
 examples/ex-tnpair/tnpair.nix | 1 +
 2 files changed, 2 insertions(+)

(limited to 'examples')

diff --git a/examples/call.nix b/examples/call.nix
index 8c4f073..8a38fdb 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -12,6 +12,7 @@ with lib;
 let
   preprocess = flip pipe [
     (bwa.align { inherit ref; })
+    (samtools.sort { nameSort = true; })
     (samtools.fixmate {})
     (samtools.sort {})
     (samtools.markdup {})
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 70f5514..9e6befe 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -12,6 +12,7 @@ let
   preprocess = s: pipe s [
     fetch
     (align { preset = "sr"; ref = ref.grch38.seq; flags = "-R'@RG\\tID:${s.type}\\tSM:${s.type}'"; })
+    (sort { nameSort = true; })
     (fixmate {})
     (sort { })
     (markdup { })
-- 
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