From fdcf948c93ee5a3a3f00e38f5d4fed7bc964a56b Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Wed, 24 Oct 2018 21:53:12 +1100
Subject: Add merge to samtools.

---
 tools/samtools-merge.nix | 28 ++++++++++++++++++++++++++++
 tools/samtools.nix       |  1 +
 2 files changed, 29 insertions(+)
 create mode 100644 tools/samtools-merge.nix

(limited to 'tools')

diff --git a/tools/samtools-merge.nix b/tools/samtools-merge.nix
new file mode 100644
index 0000000..6d072b0
--- /dev/null
+++ b/tools/samtools-merge.nix
@@ -0,0 +1,28 @@
+{ bionix
+, nixpkgs
+, flags ? null
+, outfmt ? null
+}:
+
+inputs:
+
+with nixpkgs;
+with lib;
+
+let
+  inherit (bionix.types) matchFiletype option-sort;
+  inputIsSorted = input: matchFiletype "samtools-merge" {
+       bam = _: true; #{sorting, ...}: sorting == option-sort.some (bionix.types.sorting.coord {});
+     } input;
+in
+
+assert (all inputIsSorted inputs);
+
+stdenv.mkDerivation {
+  name = "samtools-merge";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    samtools merge ${optionalString (flags != null) flags} $out ${concatStringsSep " " inputs}
+  '';
+  passthru.filetype = (builtins.elemAt inputs 0).filetype;
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 89a96b0..a05f53a 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -8,4 +8,5 @@ with bionix;
   flagstat = callBionix ./samtools-flagstat.nix;
   index = callBionix ./samtools-index.nix;
   sort = callBionix ./samtools-sort.nix;
+  merge = callBionix ./samtools-merge.nix;
 }
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