From 32c842e7c5fe1038cec73da3e07ba12df6295549 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 3 Dec 2021 09:42:04 +1100
Subject: genmap: init

---
 default.nix              |  1 +
 test-tnpair.nix          |  1 +
 tools/genmap-calcmap.nix | 22 ++++++++++++++++++++++
 tools/genmap-index.nix   | 16 ++++++++++++++++
 tools/genmap.nix         |  9 +++++++++
 5 files changed, 49 insertions(+)
 create mode 100644 tools/genmap-calcmap.nix
 create mode 100644 tools/genmap-index.nix
 create mode 100644 tools/genmap.nix

diff --git a/default.nix b/default.nix
index 59357b2..db5d14f 100644
--- a/default.nix
+++ b/default.nix
@@ -50,6 +50,7 @@ let
       lastal = callBionix ./tools/last.nix { };
       whisper = callBionix ./tools/whisper.nix { };
       star = callBionix ./tools/star.nix { };
+      genmap = callBionix ./tools/genmap.nix { };
 
       slurm-run = callPackage ./lib/slurm.nix { };
       slurm-exec = f: x: y:
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 9ba0e51..0960b6f 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -95,6 +95,7 @@ let
     snver = snver.call { ploidy = 1; } tnpairResult.alignments;
     mosdepth = mosdepth.plot { } { inputs = mapAttrsToList (_: mosdepth.depth { }) tnpairResult.alignments; names = [ "seq1" "seq2" ]; };
     xenomapper = xenomapper.allocate { } { primary = nameSort tnpairResult.alignments.tumour; secondary = nameSort tnpairResult.alignments.tumour; };
+    genmap = genmap.calcmap { } ref;
     inherit alignments;
   };
 
diff --git a/tools/genmap-calcmap.nix b/tools/genmap-calcmap.nix
new file mode 100644
index 0000000..df9ccc3
--- /dev/null
+++ b/tools/genmap-calcmap.nix
@@ -0,0 +1,22 @@
+{ bionix
+, k ? 30
+, e ? 2
+}:
+
+with bionix;
+
+ref: stage {
+  name = "genmap-mappability";
+  buildInputs = with pkgs; [ genmap ];
+  buildCommand = ''
+    mkdir $out
+    genmap map \
+      -K ${toString k} \
+      -E ${toString e} \
+      --wig \
+      -I ${bionix.genmap.index {} ref} \
+      -O $out \
+      -T $NIX_BUILD_CORES
+  '';
+  passthru.multicore = true;
+}
diff --git a/tools/genmap-index.nix b/tools/genmap-index.nix
new file mode 100644
index 0000000..249f061
--- /dev/null
+++ b/tools/genmap-index.nix
@@ -0,0 +1,16 @@
+{ bionix }:
+
+with bionix;
+with lib.types;
+
+let
+  fa = f: matchFiletype "genmap-index" { fa = _: f; } f;
+in
+
+ref: stage {
+  name = "genmap-index";
+  buildInputs = with pkgs; [ genmap ];
+  buildCommand = ''
+    genmap index -F ${fa ref} -I $out
+  '';
+}
diff --git a/tools/genmap.nix b/tools/genmap.nix
new file mode 100644
index 0000000..c29d74c
--- /dev/null
+++ b/tools/genmap.nix
@@ -0,0 +1,9 @@
+{ bionix }:
+
+with bionix;
+
+{
+  index = callBionixE ./genmap-index.nix;
+  calcmap = callBionixE ./genmap-calcmap.nix;
+}
+
-- 
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