NAME

       bgzip - Block compression/decompression utility

SYNOPSIS

       bgzip  [-cdfhikrt]  [-b virtualOffset] [-I index_name] [-l compression_level] [-o outfile]
       [-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. When multiple files are given as input, the
       operation is performed on all of them. Access and modification time  of  input  file  from
       filesystem  is  set  to  output file.  Note, access time may get updated by system when it
       deems appropriate.

OPTIONS

       --binary  Bgzip will attempt to ensure BGZF blocks end on a newline when the  input  is  a
                 text  file.   The exception to this is where a single line is larger than a BGZF
                 block (64Kb).  This can aid tools that use the index to perform random access on
                 the compressed stream, as the start of a block is likely to also be the start of
                 a text record.

                 This option processes text files as if they were binary  content,  ignoring  the
                 location  of newlines.  This also restores the behaviour for text files to bgzip
                 version 1.15 and earlier.

       -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.

       -g, --rebgzip
                 Try  to  use  an  existing index to create a compressed file with matching block
                 offsets.  The index must be specified using the -I file.gzi option.   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.

       -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.

       -k, --keep
                 Do not delete input file during operation.

       -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]

       -o, --output FILE
                 Write to a file, keep original files unchanged, will overwrite an existing file.

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

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

       -t, --test
                 Test the integrity of the compressed file.

       -@, --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.

SEE ALSO

       gzip(1), tabix(1)