|Problems? Is your data what you think it is?|
Just thought I'd add a note here since this is popping up fairly high on Google searches for bgzip. Bgzip uses the the BGZF format which is a fully backward compliant but application specific extension of gzip. In other words you can unzip a bgzipped file with gunzip, but you can't create one with gzip.
The addition that bgzip adds is block level compression. You can use the library to compress and uncompress input data in blocks which provides for a level of random access to the compressed file. The format was developed by Bob Handsaker of the Broad Institute for use in genomics/bioinformatics applications. It has been modified and used by Bob and Heng Li (also currently at the Broad) in next-generation sequence alignment and sequence variant analysis tools developed as part of the 1,000 genomes project. Application such as the BAM file format, samtools, and tabix use bgzip/BGZF to compress sequence alignment and sequence variant files and allow rapid random access to the data compressed within those files.
There are perl libraries that provide an API to files compressed in BAM and to the tabix library.http://search.cpan.org/~lds/Bio-SamTools-1.33/lib/Bio/DB/Bam/Alignment.pm
For more information see:http://samtools.sourceforge.net/
The SeqAnswers.com forum would be a good place for questions about the format and it's applications as the authors and many users are active there.