implement types

1 files changed, 58 insertions, 0 deletions

diff --git a/tools/compression.nix b/tools/compression.nix
new file mode 100644
index 0000000..aea7e13
--- /dev/null
+++ b/tools/compression.nix
@@ -0,0 +1,58 @@
+{bionix, nixpkgs}:
+
+with nixpkgs;
+with bionix;
+
+{
+  uncompress = f: types.matchFiletype "uncompress" {
+    fa = _: f;
+    fq = _: f;
+    bam = _: f;
+    sam = _: f;
+    cram = _: f;
+    vcf = _: f;
+    bed = _: f;
+    gz = _: types.tagFiletype (types.gunzip f.filetype) (stdenv.mkDerivation {
+      name = "gunzip";
+      buildCommand = "gunzip < ${f} > $out";
+    });
+    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stdenv.mkDerivation {
+      name = "bunzip2";
+      buildCommand = "bunzip2 < ${f} > $out";
+    });
+  } f.filetype;
+
+  gzip = f:
+    let
+      gz = (stdenv.mkDerivation {
+        name = "gzip";
+        buildCommand = "gzip < ${f} > $out";
+        passthru = { filetype = types.filetype.gz f.filetype; };
+      });
+    in types.matchFiletype "compressed" {
+      fa = _: gz;
+      fq = _: gz;
+      bam = _: gz;
+      sam = _: gz;
+      cram = _: gz;
+      vcf = _: gz;
+      bed = _: gz;
+    } f;
+
+  bzip2 = f:
+    let
+      bz2 = (stdenv.mkDerivation {
+        name = "bzip2";
+        buildCommand = "bzip2 < ${f} > $out";
+        passthru = { filetype = types.filetype.bz2 f.filetype; };
+      });
+    in types.matchFiletype "compressed" {
+      fa = _: gz;
+      fq = _: gz;
+      bam = _: gz;
+      sam = _: gz;
+      cram = _: gz;
+      vcf = _: gz;
+      bed = _: gz;
+    } f;
+}