From 6a4e278ef941a687d704261c903b95d4b63cf334 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 23 Feb 2021 08:21:32 +1100
Subject: samtools-view: support specifying outfmt via strings

---
 tools/samtools-view.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
index e1ca0a8..35a3fcb 100644
--- a/tools/samtools-view.nix
+++ b/tools/samtools-view.nix
@@ -13,7 +13,7 @@ with types;
 assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _: true; } input);
 
 let
-  outfmtR = if outfmt != null then outfmt input else input.filetype;
+  outfmtR = if outfmt != null then (if builtins.typeOf outfmt == "string" then { "bam" = toBam; "cram" = toCram; "sam" = toSam; }."${outfmt}" else outfmt) input else input.filetype;
   fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
   outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
 in stage {
-- 
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