Ubuntu Manpage: bgzip - Block compression/decompression utility

Provided by: tabix_1.13+ds-2build1_amd64

NAME

       bgzip - Block compression/decompression utility

SYNOPSIS

       bgzip [-cdfhir] [-b virtualOffset] [-I index_name] [-l compression_level] [-s size] [-@ threads] [file]

DESCRIPTION

       Bgzip compresses files in a similar manner to, and compatible with, gzip(1).  The file is compressed into
       a  series of small (less than 64K) 'BGZF' blocks.  This allows indexes to be built against the compressed
       file and used to retrieve portions of the data without having to decompress the entire file.

       If no files are specified on the command line, bgzip will compress (or decompress if  the  -d  option  is
       used)  standard input to standard output.  If a file is specified, it will be compressed (or decompressed
       with -d).  If the -c option is used, the result will  be  written  to  standard  output,  otherwise  when
       compressing bgzip will write to a new file with a .gz suffix and remove the original.  When decompressing
       the  input  file  must  have  a  .gz  suffix, which will be removed to make the output name.  Again after
       decompression completes the input file will be removed.

OPTIONS

-b, --offset INT
Decompress to standard output from virtual file position (0-based uncompressed offset).
Implies -c and -d.

-c, --stdout
Write to standard output, keep original files unchanged.

-d, --decompress
Decompress.

-f, --force
Overwrite files without asking, or decompress files that don't have a known compression
filename extension (e.g., .gz) without asking. Use --force twice to do both without asking.

-h, --help
Displays a help message.

-i, --index
Create a BGZF index while compressing. Unless the -I option is used, this will have the name
of the compressed file with .gzi appended to it.

-I, --index-name FILE
Index file name.

-l, --compress-level INT
Compression level to use when compressing. From 0 to 9, or -1 for the default level set by the
compression library. [-1]

-r, --reindex
Rebuild the index on an existing compressed file.

-g, --rebgzip
Try to use an existing index to create a compressed file with matching block offsets. Note
that this assumes that the same compression library and level are in use as when making the
original file. Don't use it unless you know what you're doing.

-s, --size INT
Decompress INT bytes (uncompressed size) to standard output. Implies -c.

-@, --threads INT
Number of threads to use [1].

BGZF FORMAT

       The  BGZF  format  written  by  bgzip  is  described  in  the  SAM  format  specification  available from
       http://samtools.github.io/hts-specs/SAMv1.pdf.

       It makes use of a gzip feature which allows compressed files to  be  concatenated.   The  input  data  is
       divided  into  blocks  which are no larger than 64 kilobytes both before and after compression (including
       compression headers).  Each block is compressed into a gzip file.  The gzip header includes an extra sub-
       field with identifier 'BC' and the length of the compressed block, including all headers.

GZI FORMAT

       The index format is a binary file listing pairs of compressed and uncompressed offsets in  a  BGZF  file.
       Each compressed offset points to the start of a BGZF block.  The uncompressed offset is the corresponding
       location in the uncompressed data stream.

       All values are stored as little-endian 64-bit unsigned integers.

       The file contents are:

           uint64_t number_entries

       followed by number_entries pairs of:

           uint64_t compressed_offset
           uint64_t uncompressed_offset

EXAMPLES

           # Compress stdin to stdout
           bgzip < /usr/share/dict/words > /tmp/words.gz

           # Make a .gzi index
           bgzip -r /tmp/words.gz

           # Extract part of the data using the index
           bgzip -b 367635 -s 4 /tmp/words.gz

           # Uncompress the whole file, removing the compressed copy
           bgzip -d /tmp/words.gz

AUTHOR

       The  BGZF  library  was  originally  implemented by Bob Handsaker and modified by Heng Li for remote file
       access and in-memory caching.