tarindexer VS indexed_gzip

The bioinformatics community uses block based gzip compression (bgzip) [0]. The gzip standard allows for blocks so, using an additional index file, you can use it to seek to arbitrary locations and uncompress the block.

gzip compression is maybe not optimal now and the block segmentation reduces the efficiency even further.

Though not very standard, there is also a tar indexer program [1] that allows you to create an index on tar files to do the same.

My information is at least a couple years old so things may have changed.

[0] http://www.htslib.org/doc/bgzip.html

[1] https://github.com/devsnd/tarindexer

The pieces are there. https://github.com/devsnd/tarindexer/blob/master/tarindexer.py is a prototype of indexing and seeking a tar file in python. https://github.com/pauldmccarthy/indexed_gzip allows indexing and seeking a gzip file. If those pieces of code were combined it could give you efficient targeted file extraction, but you'd need to find a coder with enough time and motivation to fuss with it.

There exists a utility called tarindexer [0] that can be used for random access to tar files. An index text file is created (one time) that is used to record the position of the files in the tar archive. Random reads are done by loading the index file and then seeking to the location of the file in question.

For random access to gzip'd files, bgzip [1] can be used. bgzip also uses an index file (one time creation) that is used to record key points for random access.

[0] https://github.com/devsnd/tarindexer

[1] http://www.htslib.org/doc/bgzip.html

Pragzip actually decompress in parallel and also access at random. I did a Show HN here: https://news.ycombinator.com/item?id=32366959

indexed_gzip https://github.com/pauldmccarthy/indexed_gzip can also do random access but is not parallel.

Both have to do a linear scan first though. The implementations however can do the linear scan on-demand, i.e., they scan only as far as needed.

bzip2 works very well with this approach. xz only works with this approach when compressed with multiple blocks. Similar is true for zstd.

For zstd, there also exists a seekable variant, which stores the block index at the end as metadata to avoid the linear scan. indexed_zstd offers random access to those files https://github.com/martinellimarco/indexed_zstd

I wrote pragzip and also combined all of the other random access compression backends in ratarmount to offer random access to TAR files that is magnitudes faster than archivemount: https://github.com/mxmlnkn/ratarmount

The pieces are there. https://github.com/devsnd/tarindexer/blob/master/tarindexer.py is a prototype of indexing and seeking a tar file in python. https://github.com/pauldmccarthy/indexed_gzip allows indexing and seeking a gzip file. If those pieces of code were combined it could give you efficient targeted file extraction, but you'd need to find a coder with enough time and motivation to fuss with it.