diff options
Diffstat (limited to 'tools/compression.nix')
| -rw-r--r-- | tools/compression.nix | 28 |
1 files changed, 26 insertions, 2 deletions
diff --git a/tools/compression.nix b/tools/compression.nix index c9c8777..b32d057 100644 --- a/tools/compression.nix +++ b/tools/compression.nix @@ -20,6 +20,7 @@ in vcf = _: f; bed = _: f; gz = _: gunzip attrs f; + bgz = _: gunzip attrs f; bz2 = _: bunzip2 attrs f; } f; @@ -36,10 +37,31 @@ in cram = _: gz; vcf = _: gz; bed = _: gz; - gz = x: x; + 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 @@ -52,7 +74,9 @@ in cram = _: gz; vcf = _: gz; bed = _: gz; - bz2 = x: x; + bz2 = _: f; + bgz = _: with compression; bzip2 { } (uncompress { } f); + gz = _: with compression; bzip2 { } (uncompress { } f); } f; } |