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generated by cgit v1.2.3 (git 2.25.1) at 2026-04-26 04:38:14 +0000
125%; } td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } .highlight .hll { background-color: #ffffcc } .highlight .c { color: #888 } /* Comment */ .highlight .err { color: #A61717; background-color: #E3D2D2 } /* Error */ .highlight .k { color: #080; font-weight: bold } /* Keyword */ .highlight .ch { color: #888 } /* Comment.Hashbang */ .highlight .cm { color: #888 } /* Comment.Multiline */ .highlight .cp { color: #C00; font-weight: bold } /* Comment.Preproc */ .highlight .cpf { color: #888 } /* Comment.PreprocFile */ .highlight .c1 { color: #888 } /* Comment.Single */ .highlight .cs { color: #C00; font-weight: bold; background-color: #FFF0F0 } /* Comment.Special */ .highlight .gd { color: #000; background-color: #FDD } /* Generic.Deleted */ .highlight .ge { font-style: italic } /* Generic.Emph */ .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ .highlight .gr { color: #A00 } /* Generic.Error */ .highlight .gh { color: #333 } /* Generic.Heading */ .highlight .gi { color: #000; background-color: #DFD } /* Generic.Inserted */ .highlight .go { color: #888 } /* Generic.Output */ .highlight .gp { color: #555 } /* Generic.Prompt */ .highlight .gs { font-weight: bold } /* Generic.Strong */ .highlight .gu { color: #666 } /* Generic.Subheading */ .highlight .gt { color: #A00 } /* Generic.Traceback */ .highlight .kc { color: #080; font-weight: bold } /* Keyword.Constant */ .highlight .kd { color: #080; font-weight: bold } /* Keyword.Declaration */ .highlight .kn { color: #080; font-weight: bold } /* Keyword.Namespace */ .highlight .kp { color: #080 } /* Keyword.Pseudo */ .highlight .kr { color: #080; font-weight: bold } /* Keyword.Reserved */ .highlight .kt { color: #888; font-weight: bold } /* Keyword.Type */ .highlight .m { color: #00D; font-weight: bold } /* Literal.Number */ .highlight .s { color: #D20; background-color: #FFF0F0 } /* Literal.String */ .highlight .na { color: #369 } /* Name.Attribute */ .highlight .nb { color: #038 } /* Name.Builtin */ .highlight .nc { color: #B06; font-weight: bold } /* Name.Class */ .highlight .no { color: #036; font-weight: bold } /* Name.Constant */ .highlight .nd { color: #555 } /* Name.Decorator */ .highlight .ne { color: #B06; font-weight: bold } /* Name.Exception */ .highlight .nf { color: #06B; font-weight: bold } /* Name.Function */ .highlight .nl { color: #369; font-style: italic } /* Name.Label */ .highlight .nn { color: #B06; font-weight: bold } /* Name.Namespace */ .highlight .py { color: #369; font-weight: bold } /* Name.Property */ .highlight .nt { color: #B06; font-weight: bold } /* Name.Tag */ .highlight .nv { color: #369 } /* Name.Variable */ .highlight .ow { color: #080 } /* Operator.Word */ .highlight .w { color: #BBB } /* Text.Whitespace */ .highlight .mb { color: #00D; font-weight: bold } /* Literal.Number.Bin */ .highlight .mf { color: #00D; font-weight: bold } /* Literal.Number.Float */ .highlight .mh { color: #00D; font-weight: bold } /* Literal.Number.Hex */ .highlight .mi { color: #00D; font-weight: bold } /* Literal.Number.Integer */ .highlight .mo { color: #00D; font-weight: bold } /* Literal.Number.Oct */ .highlight .sa { color: #D20; background-color: #FFF0F0 } /* Literal.String.Affix */ .highlight .sb { color: #D20; background-color: #FFF0F0 } /* Literal.String.Backtick */ .highlight .sc { color: #D20; background-color: #FFF0F0 } /* Literal.String.Char */ .highlight .dl { color: #D20; background-color: #FFF0F0 } /* Literal.String.Delimiter */ .highlight .sd { color: #D20; background-color: #FFF0F0 } /* Literal.String.Doc */ .highlight .s2 { color: #D20; background-color: #FFF0F0 } /* Literal.String.Double */ .highlight .se { color: #04D; background-color: #FFF0F0 } /* Literal.String.Escape */ .highlight .sh { color: #D20; background-color: #FFF0F0 } /* Literal.String.Heredoc */ .highlight .si { color: #33B; background-color: #FFF0F0 } /* Literal.String.Interpol */ .highlight .sx { color: #2B2; background-color: #F0FFF0 } /* Literal.String.Other */ .highlight .sr { color: #080; background-color: #FFF0FF } /* Literal.String.Regex */ .highlight .s1 { color: #D20; background-color: #FFF0F0 } /* Literal.String.Single */ .highlight .ss { color: #A60; background-color: #FFF0F0 } /* Literal.String.Symbol */ .highlight .bp { color: #038 } /* Name.Builtin.Pseudo */ .highlight .fm { color: #06B; font-weight: bold } /* Name.Function.Magic */ .highlight .vc { color: #369 } /* Name.Variable.Class */ .highlight .vg { color: #D70 } /* Name.Variable.Global */ .highlight .vi { color: #33B } /* Name.Variable.Instance */ .highlight .vm { color: #369 } /* Name.Variable.Magic */ .highlight .il { color: #00D; font-weight: bold } /* Literal.Number.Integer.Long */
{bionix}:

with bionix;
with lib;

let
  nix-adt-src = pkgs.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}";

  defError = errF: y: x: listToAttrs (map (n: nameValuePair n (errF n)) (filter (x: builtins.substring 0 1 x != "_") (attrNames x))) // y;

in
rec {
  nix-adt = import "${nix-adt-src}";
  matchFiletype = sym: y: x: if x ? filetype then matchFiletype' sym y x.filetype else abort "unknown filetype for ${sym}";
  matchFiletype' = sym: y: x: match x (defError (idft sym) y filetype);
  filetype = make-type "filetype" {
    fa = {};
    fq = {};
    bam = {ref = any; sorting = sort;};
    sam = {ref = any; sorting = sort;};
    cram = {ref = any; sorting = 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: x: match x.sorting (defError (idst sym) y sort);
  matchFileSorting = sym: y: let f = matchSorting sym y; in matchFiletype sym { bam = f; sam = f; cram = f; };
  sort = make-type "sort" {
    none = {};
    coord = {};
    name = {};
  };
  coordSort = f: matchFiletype "coordSort" { bam = x: filetype.bam (x // {sorting = sort.coord {};}); } {filetype = f;};
  nameSort = f: matchFiletype "nameSort" { bam = x: filetype.bam (x // {sorting = sort.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; };
}