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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;
bgz = _: 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 = _: f;
bgz = _: f;
bz2 = _: with compression; gzip { } (uncompress { } f);
}
f;
bgzip = attrs: f:
let gz = gzip (attrs // { block = true; }) f;
in
types.matchFiletype "compressed"
{
fa = _: gz;
fq = _: gz;
bam = _: gz;
sam = _: gz;
cram = _: gz;
vcf = _: gz;
bed = _: gz;
bgz = _: f;
gz = _: with compression; bgzip { } (uncompress { } f);
bz2 = _: with compression; bgzip { } (uncompress { } f);
}
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 = _: f;
bgz = _: with compression; bzip2 { } (uncompress { } f);
gz = _: with compression; bzip2 { } (uncompress { } f);
}
f;
}
|
