implement types

2 files changed, 69 insertions, 0 deletions

diff --git a/lib/references.nix b/lib/references.nix
index 61655cd..3614647 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -1,6 +1,7 @@
 { bionix, nixpkgs }:
 
 with nixpkgs;
+with bionix.types;
 
 rec {
   grch38 = grch38-p12;
@@ -13,6 +14,7 @@ rec {
         sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z";
       };
       buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.fa {};
     };
     blacklist = stdenvNoCC.mkDerivation {
       name = "blacklist-grch38";
@@ -21,6 +23,7 @@ rec {
         sha256 = "1lpnqq1mjidbdxj5i6x26rxa8x1rs8q3hlf0z1z49j3jsnkgffky";
       };
       buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.bed { ref = seq; };
     };
   };
 
@@ -34,6 +37,7 @@ rec {
         sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
       };
       buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.fa {};
     };
   };
 
@@ -47,6 +51,7 @@ rec {
               sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
               };
           buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa {};
       };
   };
 }
diff --git a/lib/types.nix b/lib/types.nix
new file mode 100644
index 0000000..a347046
--- /dev/null
+++ b/lib/types.nix
@@ -0,0 +1,64 @@
+{bionix, nixpkgs}:
+
+with nixpkgs;
+
+let
+  nix-adt-src = fetchFromGitHub {
+    owner = "shlevy";
+    repo = "nix-adt";
+    rev = "dd04b5d08eed65ecd73aafde56a78078e09f1c74";
+    sha256 = "0vhk1y7gilgn2pgvj4813bh2ljpw4pvrph8k8b0fsg56dbm8mqxa";
+  };
+  nix-adt = import "${nix-adt-src}";
+  inherit (nix-adt.checked) make-type match any std none;
+  inherit (std) option;
+
+  idft = sym: ft: _: abort "unhandled filetype (${ft}) for ${sym}";
+  idst = sym: st: _: abort "unhandled sorting (${st}) for ${sym}";
+
+in
+rec {
+  option-sort = option sorting;
+
+  matchFiletype = sym: y: x: if x ? filetype then match x.filetype ({
+    fa = idft sym "fasta";
+    fq = idft sym "fastq";
+    bam = idft sym "bam";
+    sam = idft sym "sam";
+    cram = idft sym "cram";
+    vcf = idft sym "vcf";
+    bed = idft sym "bed";
+    gz = idft sym "gz";
+    bz2 = idft sym "bz2";
+  } // y) else abort "unknown filetype for ${sym}";
+  filetype = make-type "filetype" {
+    fa = {};
+    fq = {};
+    bam = {ref = any; sorting = option-sort;};
+    sam = {ref = any; sorting = option-sort;};
+    cram = {ref = any; sorting = option-sort;};
+    vcf = {ref = any;};
+    bed = {ref = any;};
+    gz = filetype;
+    bz2 = filetype;
+  };
+
+  toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; cram = filetype.cram; };
+  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 { some = z: match z ( { coord = idst sym "coord"; name = idst sym "name"; } // y); none = abort "unknown sort for ${sym}"; }; in matchFiletype sym { bam = f; sam = f; cram = f; };
+  sorting = make-type "sorting" {
+    coord = {};
+    name = {};
+  };
+  coordSort = f: matchFiletype "coordSort" { bam = x: filetype.bam (x // {sorting = option-sort.some (sorting.coord {});}); } {filetype = f;};
+  nameSort = f: matchFiletype "nameSort" { bam = x: filetype.bam (x // {sorting = option-sort.some (sorting.name {});}); } {filetype = f;};
+
+  gunzip = matchFiletype "gunzip" { gz = x: x; };
+  bunzip2 = matchFiletype "bunzip2" { bz2 = x: x; };
+
+  tag = attrs: x: if x ? type && x.type == "derivation" then x // attrs else tagPassthru attrs x;
+  tagPassthru = attrs: x: if x ? passthru then x // { passthru = x.passthru // attrs; } else x // { passthru = attrs; };
+  tagFiletype = ft: tag { filetype = ft; };
+}