From ca3d5d1550d068b62dbc836b07abefc3bb06cab9 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 8 Oct 2018 14:22:50 +1100
Subject: Fix type in samtools-view
---
tools/samtools-view.nix | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
index e1cdac1..b791534 100644
--- a/tools/samtools-view.nix
+++ b/tools/samtools-view.nix
@@ -11,12 +11,12 @@ with nixpkgs;
with lib;
with bionix.types;
-assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
+assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _: true; } input);
let
outfmtR = if outfmt != null then outfmt input else input.filetype;
fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
- outfmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
+ outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
in stdenv.mkDerivation {
name = "samtools-view";
buildInputs = [ samtools ];
--
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