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{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;
gz = x: x;
} 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;
bz2 = x: x;
} f;
}
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