From 5fc4c8fc0ce707c57204e57a2cd058c019bc8bd8 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 25 Jan 2022 12:04:05 +1100
Subject: add tabix indexing

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

diff --git a/tools/samtools-tabix.nix b/tools/samtools-tabix.nix
new file mode 100644
index 0000000..a493b9d
--- /dev/null
+++ b/tools/samtools-tabix.nix
@@ -0,0 +1,22 @@
+{ bionix
+, flags ? null
+}:
+
+input:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "samtools-tabix" { bgz = _: true; } input);
+
+stage {
+
+  name = "samtools-tabix";
+  buildInputs = with pkgs; [ htslib ];
+  buildCommand = ''
+    ln -s ${input} input.bgz
+    tabix input.bgz
+    cp input.bgz.tbi $out
+  '';
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 27f3f73..e0c45dd 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -12,4 +12,5 @@ with bionix;
   merge = callBionixE ./samtools-merge.nix;
   markdup = callBionixE ./samtools-markdup.nix;
   fixmate = callBionixE ./samtools-fixmate.nix;
+  tabix = callBionixE ./samtools-tabix.nix;
 }
-- 
cgit v1.2.3