top of page
Uncompress files compressed with genozip.

 

Usage

 

genounzip [options]… [files]…

One or more file names must be given.

Examples

genounzip file1.vcf.genozip file2.sam.genozip

 

genounzip file.vcf.genozip --output file.vcf.gz

 

genounzip mysample.R1+R2.fastq.genozip --prefix=new_directory/

Options

 

-e, --reference filename.  

Load a reference file prior to decompressing. Used only for files compressed with --reference. If not provided, genounzip will use the same reference filename as used for genozip.

Note: this is equivalent of setting the environment variable $GENOZIP_REFERENCE with the reference filename.

--no-cache

Don't store reference genome data in RAM. Can also be used to delete previously cached genomes. See reference genome caching

-f, --force  

Force overwrite of the output file.

-D, --subdirs  

If a file name on the command line is a directory include all files of that directory (recursively).

-o, --output output-filename

Output to this filename.

 

Note: output-filename can also be a directory name, in which case the output file is written to the specified directory. If the name has a ‘/’ suffix (e.g. “-o my-dir/”), then the directory is created if it doesn’t already exist.

-p, --password password.  

Provide password to access file(s) that were compressed with --password.

-x, --index  

Create an index file alongside the decompressed file. The index file is created as described:

Data type   Tool used     

SAM/BAM     samtools index

FASTQ       samtools faidx

FASTA       samtools faidx

VCF         bcftools index

Other types --index not supported

-z, --bgzf level 

Compress the output to the BGZF format (.gz extension) using libdeflate at the compression level specified by the argument. level specifies the BGZF compression level from 0 (no compression) to 12 (best yet slowest compression). If you are not sure what value to choose - 6 is a popular option.

 

Use --bgzf=exact to instruct genounzip to attempt to re-create the same exact BGZF compression as in the original file. Whether genounzip succeeds in re-creating the exact same BGZF compression ratio depends on the compression library used by the application that generated the original file. See also: Compressing already-compressed files.

 

-u--prefix prefix

For FASTQ files compressed with --pair: Specify a prefix that is added to each file name. A prefix may include a directory.

 

-m, --md5  

Show the digest of the decompressed file - MD5 if the file was compressed with --md5 and Adler32 if not.

Note: for compressed files (e.g. myfile.vcf.gz) the digest calculated is that of the original uncompressed file, see:

Verifying file integrity.

 

-t, --test  

Decompress in memory (i.e. without writing the decompressed file to disk) and use the digest (MD5 or Adler32) to verify that the resulting decompressed file is identical to the original file.

-^, --replace  

Delete the genozip-compressed file after completing its decompression.

-q, --quiet  

Don't show the progress indicator or warnings.

-Q, --noisy

The --quiet option is turned on by default when outputting to the terminal. --noisy stops the suppression of warnings.

-@, --threads number

Specify the maximum number of threads. By default genozip allocates 1.1 threads per core in order to maximize usage of all available cores. An exception is on Mac and Windows (including WSL) where the default allocation is 0.75 threads per core to maintain the operating system's UI's feeling of interactivity.

Note: For genounzip and genocat this limit is only approximate. For genozip, it is strictly enforced.

--low-memory

Uses less memory than normal, but runs slower

-w, --stats

Show the internal structure of a genozip file and the associated compression statistics.

-W, --STATS

Show more detailed statistics.

 

Note: specifying -W or -w twice, results in the header line of the statistics printed to stderr, thereby surviving piping stdout to grep

 

--show-filename

Show the file name for each file.

--validate[=valid]  

Validates that the file(s) are valid genozip files. By default reports files that are invalid. With --validate=valid reports files that are valid, and if run on a single file, exit code indicates validity.

-T, --files-from filename

An alternative to providing input file names on the command line. filename it a textual file containing a newline-separated list of files. If filename is - (a hyphen) data is taken from stdin rather than a file.

--log filename

Send non-file output to a log file instead of the terminal.

--echo

Output the full command line upon successful or failed completion of execution.

--help

Show a link to this page.

-L, --license, --licence

Show the license terms and conditions for this product as accepted. Combine with --force to see the version of the license current to the version of Genozip used. If you wish to change your license to the most recent one - make sure your version of Genozip is the latest and re-register with genozip --register.

-V, --version

Display Genozip's version number

--show-reference

Show the name and MD5 of the reference file that needs to be provided to uncompress this file.

bottom of page