From 2bd2c3958ed91ef3bbea2fc3e077a8c03a648a1b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 16 May 2022 12:46:12 +1000
Subject: quip: init

---
 default.nix           |  1 +
 lib/types.nix         |  1 +
 quip.nix              |  8 ++++++++
 test-tnpair.nix       |  1 +
 tools/quip-app.nix    | 19 +++++++++++++++++++
 tools/quip-quip.nix   | 17 +++++++++++++++++
 tools/quip-unquip.nix | 18 ++++++++++++++++++
 tools/quip.nix        |  6 ++++++
 8 files changed, 71 insertions(+)
 create mode 100644 quip.nix
 create mode 100644 tools/quip-app.nix
 create mode 100644 tools/quip-quip.nix
 create mode 100644 tools/quip-unquip.nix
 create mode 100644 tools/quip.nix

diff --git a/default.nix b/default.nix
index 73cccdd..62b6d3c 100644
--- a/default.nix
+++ b/default.nix
@@ -54,6 +54,7 @@ let
       subread = callBionix ./tools/subread.nix { };
       hatchet = callBionix ./tools/hatchet.nix { };
       pizzly = callBionix ./tools/pizzly.nix { };
+      quip = callBionix ./tools/quip.nix { };
 
       slurm-run = callPackage ./lib/slurm.nix { };
       slurm-exec = f: x: y:
diff --git a/lib/types.nix b/lib/types.nix
index 11f4bf4..896c39c 100644
--- a/lib/types.nix
+++ b/lib/types.nix
@@ -35,6 +35,7 @@ rec {
     gz = filetype;
     bgz = filetype;
     bz2 = filetype;
+    qp = filetype;
   };
 
   toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; inherit (filetype) cram; };
diff --git a/quip.nix b/quip.nix
new file mode 100644
index 0000000..c5e7186
--- /dev/null
+++ b/quip.nix
@@ -0,0 +1,8 @@
+{bionix}:
+with bionix;
+
+{
+app = callPackage ./quip-app.nix {};
+quip = callBionix ./quip-quip.nix;
+unquip = callBionix ./quip-unqip.nix;
+}
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 679cc67..169d531 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -98,6 +98,7 @@ 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; };
+    quip = with quip; unquip {} (quip {} tnpairResult.alignments.tumour);
     genmap = genmap.calcmap { } ref;
     inherit alignments;
   };
diff --git a/tools/quip-app.nix b/tools/quip-app.nix
new file mode 100644
index 0000000..422b603
--- /dev/null
+++ b/tools/quip-app.nix
@@ -0,0 +1,19 @@
+{
+  stdenv,
+  fetchFromGitHub,
+  autoreconfHook,
+  zlib,
+}:
+stdenv.mkDerivation rec {
+  name = "quip";
+
+  src = fetchFromGitHub {
+    owner = "dcjones";
+    repo = "quip";
+    rev = "9165bb5ac17a2cf2822e437df573487d7adfa1cc";
+    sha256 = "PpvgLzdiYcLyJ1JH9UzbUd29eKIlyY440HiJGYWvkrs=";
+  };
+
+  nativeBuildInputs = [autoreconfHook];
+  buildInputs = [zlib];
+}
diff --git a/tools/quip-quip.nix b/tools/quip-quip.nix
new file mode 100644
index 0000000..77cf557
--- /dev/null
+++ b/tools/quip-quip.nix
@@ -0,0 +1,17 @@
+{bionix}:
+with bionix;
+with lib.types;
+  input: let
+    ref = matchFiletype "quip" {bam = f: f.ref;} input;
+  in
+    stage {
+      name = "quip";
+      buildInputs = [quip.app];
+      buildCommand = ''
+        ln -s ${input} input.bam
+        quip -r ${ref} input.bam
+        cp input.bam.qp $out
+      '';
+      stripStorePaths = false;
+      passthru.filetype = filetype.qp input.filetype;
+    }
diff --git a/tools/quip-unquip.nix b/tools/quip-unquip.nix
new file mode 100644
index 0000000..8c9cc01
--- /dev/null
+++ b/tools/quip-unquip.nix
@@ -0,0 +1,18 @@
+{bionix}:
+with bionix;
+with lib.types;
+  input: let
+    bamft = matchFiletype "unquip" {qp = x: x;} input;
+    ref = matchFiletype' "unquip-sub" {bam = f: f.ref;} bamft;
+  in
+    stage {
+      name = "unquip";
+      buildInputs = [quip.app];
+      buildCommand = ''
+        ln -s ${input} input.bam.qp
+        unquip -r ${ref} input.bam.qp
+        cp input.bam $out
+      '';
+      stripStorePaths = false;
+      passthru.filetype = bamft;
+    }
diff --git a/tools/quip.nix b/tools/quip.nix
new file mode 100644
index 0000000..f0a57aa
--- /dev/null
+++ b/tools/quip.nix
@@ -0,0 +1,6 @@
+{bionix}:
+with bionix; {
+  app = pkgs.callPackage ./quip-app.nix {};
+  quip = callBionix ./quip-quip.nix;
+  unquip = callBionix ./quip-unquip.nix;
+}
-- 
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