From 7f11fb044b6e08c53f53a1a0d0d6519fba1ccce3 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 29 Oct 2018 15:32:38 +1100
Subject: init: samtools-markdup

---
 tools/samtools-markdup.nix | 22 ++++++++++++++++++++++
 tools/samtools.nix         |  1 +
 2 files changed, 23 insertions(+)
 create mode 100644 tools/samtools-markdup.nix

diff --git a/tools/samtools-markdup.nix b/tools/samtools-markdup.nix
new file mode 100644
index 0000000..73094f2
--- /dev/null
+++ b/tools/samtools-markdup.nix
@@ -0,0 +1,22 @@
+{ bionix
+, nixpkgs
+, flags ? null
+}:
+
+input:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (matchFiletype "samtools-markdup" { bam = _: true; } input);
+assert (matchFileSorting "samtools-markdup" { coord = _: true; } input);
+
+stdenv.mkDerivation {
+  name = "samtools-markdup";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    samtools markdup ${optionalString (flags != null) flags} ${input} $out
+  '';
+  passthru.filetype = input.filetype;
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index e26d996..62414df 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -10,5 +10,6 @@ with bionix;
   dict = callBionix ./samtools-dict.nix;
   sort = callBionix ./samtools-sort.nix;
   merge = callBionix ./samtools-merge.nix;
+  markdup = callBionix ./samtools-markdup.nix;
   fixmate = callBionix ./samtools-fixmate.nix;
 }
-- 
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