implement types

1 files changed, 27 insertions, 0 deletions

diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
new file mode 100644
index 0000000..e1cdac1
--- /dev/null
+++ b/tools/samtools-view.nix
@@ -0,0 +1,27 @@
+{ bionix
+, nixpkgs
+, nameSort ? false
+, flags ? null
+, outfmt ? null
+}:
+
+input:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
+
+let
+  outfmtR = if outfmt != null then outfmt input else input.filetype;
+  fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
+  outfmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
+in stdenv.mkDerivation {
+  name = "samtools-view";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    samtools view ${outfmtFlags} ${optionalString (flags != null) flags} ${input} > $out
+  '';
+  passthru.filetype = outfmtR;
+}