From 8df1eae273acaf97ead80b3f5ef78a387be0934b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 27 Sep 2018 21:13:35 +1000
Subject: Fix missing index for mosdepth

---
 tools/mosdepth-depth.nix | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 586cdcb..be28aaf 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,6 +1,8 @@
 { stdenv
 , lib
+, callPackage
 , mosdepth
+, index ? callPackage ./samtools-index.nix {}
 , flags ? null}:
 
 with lib;
@@ -12,6 +14,8 @@ stdenv.mkDerivation {
   buildInputs = [ mosdepth ];
   buildCommand = ''
     mkdir $out
-    mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out ${input}
+    ln -s ${input} input.bam
+    ln -s ${index input} input.bam.bai
+    mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
   '';
 }
-- 
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