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{ bionix }:
with bionix;
with lib;
let
nix-adt-src = pkgs.fetchFromGitHub {
owner = "shlevy";
repo = "nix-adt";
rev = "dd04b5d08eed65ecd73aafde56a78078e09f1c74";
sha256 = "0vhk1y7gilgn2pgvj4813bh2ljpw4pvrph8k8b0fsg56dbm8mqxa";
};
nix-adt = import "${nix-adt-src}";
inherit (nix-adt.unchecked) make-type match any std none;
inherit (std) option;
idft = sym: ft: _: abort "unhandled filetype (${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;
bgz = filetype;
bz2 = filetype;
};
toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; inherit (filetype) cram; };
toBam = matchFiletype "bam2cram" { inherit (filetype) bam; sam = filetype.bam; cram = filetype.bam; };
toSam = matchFiletype "bam2cram" { bam = filetype.sam; inherit (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; };
}
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