tools/compression.nix


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{bionix}:

with bionix;
with types;

let
  gzip = callBionixE ./compression-gzip.nix;
  gunzip = callBionixE ./compression-gunzip.nix;
  bunzip2 = callBionixE ./compression-bunzip2.nix;

in {
  uncompress = attrs: f: matchFiletype "uncompress" {
    fa = _: f;
    fq = _: f;
    bam = _: f;
    sam = _: f;
    cram = _: f;
    vcf = _: f;
    bed = _: f;
    gz = _: gunzip attrs f;
    bz2 = _: bunzip2 attrs f;
  } f;

  gzip = attrs: f:
    let gz = gzip attrs f;
    in types.matchFiletype "compressed" {
      fa = _: gz;
      fq = _: gz;
      bam = _: gz;
      sam = _: gz;
      cram = _: gz;
      vcf = _: gz;
      bed = _: gz;
      gz = x: x;
    } f;

  bzip2 = attrs: f:
    let bz2 = bzip2 attrs f;
    in types.matchFiletype "compressed" {
      fa = _: gz;
      fq = _: gz;
      bam = _: gz;
      sam = _: gz;
      cram = _: gz;
      vcf = _: gz;
      bed = _: gz;
      bz2 = x: x;
    } f;
}