From ec77e9c3a9c2dc7425ee07474f525dd0a3d01fab Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 1 Nov 2018 15:40:47 +1100
Subject: samtools-sort: don't sort if already sorted

---
 tools/samtools-sort.nix | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

(limited to 'tools/samtools-sort.nix')

diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index ab9d603..5a02dab 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -11,7 +11,7 @@ with nixpkgs;
 with lib;
 
 let
-  inherit (bionix.types) matchFiletype coordSort;
+  inherit (bionix.types) matchFiletype coordSort matchFileSorting;
 in
 
 assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
@@ -19,11 +19,20 @@ assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _:
 let
   outfmtR = if outfmt != null then outfmt input else input.filetype;
   outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;};
+  alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; } input;
 in stdenv.mkDerivation {
   name = "samtools-sort";
   buildInputs = [ samtools ];
-  buildCommand = ''
-    samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${outFmtFlags} ${optionalString (flags != null) flags} ${input} > $out
-  '';
+  buildCommand =
+    if alreadySorted then
+      "ln -s $out ${input}"
+    else
+      ''
+        samtools sort -@ $NIX_BUILD_CORES \
+          ${optionalString nameSort "-n"} \
+          ${outFmtFlags} \
+          ${optionalString (flags != null) flags} \
+          ${input} > $out
+      '';
   passthru.filetype = if nameSort then bionix.types.nameSort outfmtR else coordSort outfmtR;
 }
-- 
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