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genounzip

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 bound.vcf.genozip --prefix=new_directory/

Options

-e, --reference filename.  Load a reference file prior to decompressing. Required only for files compressed with --reference

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

-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.

-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. Argument 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. Note: by default (absent this option) genozip will attempt to re-create the same BGZF compression as in the original file. Whether genozip succeeds in re-creating the exact same BGZF compression ratio depends on the compression library used by the application that generated the original file.

-u --prefix <prefix> Specify a prefix that is added to each file component name. A prefix may include a directory.

-m, --md5  Show the digest of the decompressed file - MD5 if the file was compressed with --md5 or --test and Adler32 if not. Note: for compressed files (e.g. myfile.vcf.gz) the digest calculated is that of the original uncompressed file.

-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  Replace the source file with the result file rather than leaving it unchanged.

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

-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.

-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.

--no-PG.  (SAM BAM) When translating the file Genozip normally adds information in a @PG header line. With this option it doesn't.

General options

-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.

-h, --help  Show a link to this page.

--help=attributions  Show attributions.

-L, --license, --licence  Show the license terms and conditions for this product as accepted. Combine with --force to see the most up-do-date version of the license. If you wish to change your license to the most recent one - re-register with genozip --register.

-V, --version  Display Genozip's version number.