1bgzip(1)                     Bioinformatics tools                     bgzip(1)
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NAME

6       bgzip - Block compression/decompression utility
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SYNOPSIS

9       bgzip   [-cdfhir]  [-b  virtualOffset]  [-I  index_name]  [-l  compres‐
10       sion_level] [-s size] [-@ threads] [file]
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DESCRIPTION

13       Bgzip compresses files in a similar manner  to,  and  compatible  with,
14       gzip(1).  The file is compressed into a series of small (less than 64K)
15       'BGZF' blocks.  This allows indexes to be built against the  compressed
16       file and used to retrieve portions of the data without having to decom‐
17       press the entire file.
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19       If no files are specified on the command line, bgzip will compress  (or
20       decompress if the -d option is used) standard input to standard output.
21       If a file is specified, it will be  compressed  (or  decompressed  with
22       -d).   If the -c option is used, the result will be written to standard
23       output, otherwise when compressing bgzip will write to a new file  with
24       a  .gz  suffix  and  remove the original.  When decompressing the input
25       file must have a .gz suffix, which will be removed to make  the  output
26       name.   Again  after  decompression  completes  the  input file will be
27       removed.
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OPTIONS

31       -b, --offset INT
32                 Decompress to standard  output  from  virtual  file  position
33                 (0-based uncompressed offset).  Implies -c and -d.
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35       -c, --stdout
36                 Write to standard output, keep original files unchanged.
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38       -d, --decompress
39                 Decompress.
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41       -f, --force
42                 Overwrite files without asking.
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44       -h, --help
45                 Displays a help message.
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47       -i, --index
48                 Create  a BGZF index while compressing.  Unless the -I option
49                 is used, this will have the name of the compressed file  with
50                 .gzi appended to it.
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52       -I, --index-name FILE
53                 Index file name.
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55       -l, --compress-level INT
56                 Compression  level  to use when compressing.  From 0 to 9, or
57                 -1 for the default level set by the compression library. [-1]
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59       -r, --reindex
60                 Rebuild the index on an existing compressed file.
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62       -g, --rebgzip
63                 Try to use an existing index to create a compressed file with
64                 matching block offsets.  Note that this assumes that the same
65                 compression library and level are in use as when  making  the
66                 original  file.   Don't  use  it  unless you know what you're
67                 doing.
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69       -s, --size INT
70                 Decompress INT bytes (uncompressed size) to standard  output.
71                 Implies -c.
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73       -@, --threads INT
74                 Number of threads to use [1].
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BGZF FORMAT

77       The  BGZF format written by bgzip is described in the SAM format speci‐
78       fication available from http://samtools.github.io/hts-specs/SAMv1.pdf.
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80       It makes use of a gzip feature which allows compressed files to be con‐
81       catenated.   The  input data is divided into blocks which are no larger
82       than 64 kilobytes both before and after compression (including compres‐
83       sion  headers).   Each  block is compressed into a gzip file.  The gzip
84       header includes an extra sub-field with identifier 'BC' and the  length
85       of the compressed block, including all headers.
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GZI FORMAT

89       The  index  format  is  a  binary  file listing pairs of compressed and
90       uncompressed offsets in a BGZF file.  Each compressed offset points  to
91       the  start of a BGZF block.  The uncompressed offset is the correspond‐
92       ing location in the uncompressed data stream.
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94       All values are stored as little-endian 64-bit unsigned integers.
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96       The file contents are:
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98           uint64_t number_entries
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100       followed by number_entries pairs of:
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102           uint64_t compressed_offset
103           uint64_t uncompressed_offset
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EXAMPLES

108           # Compress stdin to stdout
109           bgzip < /usr/share/dict/words > /tmp/words.gz
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111           # Make a .gzi index
112           bgzip -r /tmp/words.gz
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114           # Extract part of the data using the index
115           bgzip -b 367635 -s 4 /tmp/words.gz
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117           # Uncompress the whole file, removing the compressed copy
118           bgzip -d /tmp/words.gz
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AUTHOR

123       The BGZF library was originally implemented by Bob Handsaker and  modi‐
124       fied by Heng Li for remote file access and in-memory caching.
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SEE ALSO

128       gzip(1), tabix(1)
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132htslib-1.9                       18 July 2018                         bgzip(1)
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