From 99ee99c490cc109b78986181ee1be4ce1cd0c0ed Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 25 Oct 2018 08:02:20 +1100
Subject: Improve type safety of samtools-merge

---
 lib/types.nix            | 3 ++-
 test-tnpair.nix          | 1 +
 tools/samtools-index.nix | 2 +-
 tools/samtools-merge.nix | 8 +++-----
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/types.nix b/lib/types.nix
index 2e5adca..4dbc6ff 100644
--- a/lib/types.nix
+++ b/lib/types.nix
@@ -38,7 +38,8 @@ rec {
   toBam = matchFiletype "bam2cram" { bam = filetype.bam; sam = filetype.bam; cram = filetype.bam; };
   toSam = matchFiletype "bam2cram" { bam = filetype.sam; sam = filetype.sam; cram = filetype.sam; };
 
-  matchSorting = sym: y: let f = x: match x.sorting (defError (idst sym) y sort); in matchFiletype sym { bam = f; sam = f; cram = f; };
+  matchSorting = sym: y: x: match x.sorting (defError (idst sym) y sort);
+  matchFileSorting = sym: y: let f = matchSorting sym y; in matchFiletype sym { bam = f; sam = f; cram = f; };
   sort = make-type "sort" {
     none = {};
     coord = {};
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 7deaf3b..0f6a441 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -54,6 +54,7 @@ let
       ln -s ${tnpairResult.variants} $out/strelka
       mkdir $out/alignments
       ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss
+      ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam
       ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram
       ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram
       ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index aad46a7..6919f97 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -10,7 +10,7 @@ with lib;
 with bionix.types;
 
 assert (matchFiletype "samtools-index" { bam = _: true; } input);
-assert (matchSorting "samtools-index" { coord = _: true; } input);
+assert (matchFileSorting "samtools-index" { coord = _: true; } input);
 
 stdenv.mkDerivation {
   name = "samtools-index";
diff --git a/tools/samtools-merge.nix b/tools/samtools-merge.nix
index 6d072b0..eacf520 100644
--- a/tools/samtools-merge.nix
+++ b/tools/samtools-merge.nix
@@ -10,13 +10,11 @@ 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;
+  inherit (bionix.types) matchFiletype matchSorting;
+  inputIsHomogenous = length (unique (map (matchFiletype "samtools-merge" {bam = x: x // {sorting = matchSorting "samtools-merge" {coord = _: "coord";} x;};}) inputs)) == 1;
 in
 
-assert (all inputIsSorted inputs);
+assert inputIsHomogenous;
 
 stdenv.mkDerivation {
   name = "samtools-merge";
-- 
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