Uncompress files compressed with genozip.
Usage
genounzip [options]… [files]…
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One or more file names must be given.
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Examples
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genounzip file1.vcf.genozip file2.sam.genozip
genounzip file.vcf.genozip --output file.vcf.gz
genounzip mysample.R1+R2.fastq.genozip --prefix=new_directory/
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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.
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Note: this is equivalent of setting the environment variable $GENOZIP_REFERENCE with the reference filename.
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Note: if $GENOZIP_REFERENCE is set to a directory name, then the reference file is sought in that directory, with the reference file name used during compression. If it is not found there, the reference file path used for compression is used.
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--no-cache
Don't store reference genome data in RAM. Can also be used to delete previously cached genomes. See reference genome caching.
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-f, --force
Force overwrite of the output file.
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-D, --subdirs
If a file name on the command line is a directory include all files of that directory (recursively).
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-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.
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-p, --password password.
Provide password to access file(s) that were compressed with --password.
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-x, --index
Create an index file alongside the uncompressed file. This option is set by default for bam, sam.gz and vcf.gz files, and is optional for FASTQ and FASTA files. See indexing for more details.
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--no-bai
--no-tbi
Don't create a bai or tbi index file. This option does not result in faster uncompression. See indexing for more details.
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-z, --bgzf [level|exact|exact-strict]
Controls the details of the re-compression of the output to gzip format (.gz or .bam extension). level specifies the gz-recompression level from 0 (no compression) to 5 (best yet slowest compression). The default level is 2.
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--bgzf=exact to instruct genounzip to attempt to gz-recompress to the exact same gz-compression as the original file. Whether genounzip succeeds to do so depends on the gzip library used by the tool that created the original file. See Compressing already-compressed files.
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--bgzf=exact-strict is the same as --bgzf=exact except that the process exits with an error if exact gz-recompression is not possible.
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-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:
-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.
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-^, --replace
Delete the genozip-compressed file after completing its decompression.
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-q, --quiet
Don't show the progress indicator or warnings.
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-Q, --noisy
The --quiet option is turned on by default when outputting to the terminal. --noisy stops the suppression of warnings.
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-@, --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.
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Note: For genounzip and genocat this limit is only approximate. For genozip, it is strictly enforced.
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--low-memory
Uses less memory than normal, but runs slower
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-w, --stats
Show the internal structure of a genozip file and the associated compression statistics.
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--print-filename
Show the file name for each file.
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--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.
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-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.
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--log filename
Send non-file output to a log file instead of the terminal.
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--echo [=arbitrary-text]
Output the full command line upon successful or failed completion of execution. Useful if logging output.
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It is possible to add an optional argument that has no effect other than to be shown on the command line outputted – this can be useful for adding contextual information when logging the output.
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--help
Show a link to this page.
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-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.
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-V, --version
Display Genozip's version number
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--print-reference
Show the name and MD5 of the reference file that needs to be provided to uncompress this file.
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