From bae57d22d7a626c12660f966eba0d2514d376860 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 10 Aug 2020 09:41:10 +1000
Subject: bwa: alt regex generalisation

---
 tools/bwa-index.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index 17b651f..65d9bd5 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -1,5 +1,6 @@
 { bionix
 , flags ? null
+, altRegex ? "^>.*_alt$"
 }:
 
 ref:
@@ -18,6 +19,7 @@ stage {
     bwa index ${optionalString (flags != null) flags} ref.fa
     mkdir $out
     mv ref.fa.* $out
-    grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true
+    grep -P '${altRegex}' ref.fa | tr -d '^>' > $out/idxbase.alt || true
   '';
+  stripStorePaths = false;
 }
-- 
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