From a75e95881c49cfa52cc47c27a4980b2381cc0fbf Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 27 Sep 2018 15:41:09 +1000
Subject: Allow flag passing to bwa index

---
 tools/bwa-index.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index b5e3779..3329221 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -1,6 +1,7 @@
 { stdenv
 , lib
 , bwa
+, flags ? null
 }:
 
 ref:
@@ -12,7 +13,7 @@ stdenv.mkDerivation {
   buildInputs = [ bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
-    bwa index ref.fa
+    bwa index ${optionalString (flags != null) flags} ref.fa
     mkdir $out
     mv ref.fa.* $out
     grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true
-- 
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