How can I get the uncompressed size of a BGZIP file ?

Question: How can I get the uncompressed size of a BGZIP file ?

8 weeks ago by

sacha • 2.0k

France

sacha • 2.0k wrote:

Reading uncompress file size from a gzip file is easy. The value is stored in the last 4 bytes of the gzip file. But it doesn't with bgzip file ! Any idea how can I get this information without uncompress the file ?

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modified 8 weeks ago by John Marshall ♦ 2.2k • written 8 weeks ago by sacha • 2.0k

8 weeks ago by

John Marshall ♦ 2.2k

Glasgow, Scotland

John Marshall ♦ 2.2k wrote:

Each block of a BGZF file is itself a valid GZIP file. So you can calculate the overall uncompressed size as the total of all those size entries recorded in the last four bytes of each GZIP member file.

It remains to find the end of each BGZF block, but fortunately each block's header contains a BC extra subfield that records the compressed length of the block. Hence you can calculate the total uncompressed size without decompressing anything and only reading about 22 bytes out of each ~64K as follows:

Read a BGZF header
Use the BC bsize field to seek to the end of the block
Read the last few bytes of the block, and add that isize field to your total
Repeat until EOF

You can find an implementation of this in C in my bgzfsize.c utility.

ADD COMMENT • link written 8 weeks ago by John Marshall ♦ 2.2k

8 weeks ago by

jukka.matilainen • 0

jukka.matilainen • 0 wrote:

If you happen to have the *.gzi index file around (bgzip -i option when compressing), you could read the uncompressed offset of the last block from the index file. This way you'll only need to decompress the last block to find its uncompressed size.

In Bash you could do it for example like this.

last_offset=$( tail -c 8 file.gz.gzi | od --endian=little -An -t u8 )
last_size=$( bgzip -b $offset file.gz | wc -c )
echo $(( $last_offset + $last_size ))

Explained: tail to read the last 8 bytes from the index file which contains the uncompressed offset of the last block and od to print is as an little-endian unsigned 64-bit integer (the format of the index file is described in the bgzip(1) man page). bgzip to uncompress from that offset onwards and wc to count the bytes in the uncompressed output.

If you don't happen to have the *.gzi index file, well, you could recreate it with bgzip -r for an existing bgzipped file, but that of course requires processing the whole (compressed) file...

ADD COMMENT • link modified 8 weeks ago • written 8 weeks ago by jukka.matilainen • 0

Is gzi same as tbi index ?

ADD REPLY • link written 8 weeks ago by sacha • 2.0k

No, a gzi index file is in a different format than a tbi tabix index file. The gzi file is produced when running bgzip with the -i switch when compressing or with the -r switch when running on an existing bgzipped file.

ADD REPLY • link modified 8 weeks ago • written 8 weeks ago by jukka.matilainen • 0

Ok ! I am asking because tbi is more common than gzi. So, I wonder if I can get this information from this index too.

ADD REPLY • link written 8 weeks ago by sacha • 2.0k

Unfortunately I am not that familiar with the tabix tbi file format. The format is documented here, and by a quick glance I would assume that in a tbi index for a bgzipped file, all the offsets would be referring to the compressed file, and not the uncompressed content, so the answer would probably then be no.

ADD REPLY • link modified 8 weeks ago • written 8 weeks ago by jukka.matilainen • 0

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