From 6664d56a18be8f0e9f027d6e5723b4b4e35f2694 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 9 Feb 2022 13:02:54 +1100
Subject: whisper: RG line support

---
 tools/whisper-align.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix
index 38bcedf..b6130bc 100644
--- a/tools/whisper-align.nix
+++ b/tools/whisper-align.nix
@@ -2,6 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
+, RG ? { }
 , indexAttrs ? { }
 }:
 
@@ -33,6 +34,7 @@ stage {
       -stdout \
       index ${fq input1} \
       ${optionalString (input2 != null) (fq input2)} \
+      ${optionalString (RG ? ID) "-rg '@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \
       > $out
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.none { }; };
-- 
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