Genozip compression is lossless relative to the underlying data, which means that the data reconstructed during uncompression is exactly identical to the original data compressed.
Verification of Losslessness
When uncompressing with
genocat, these tools verify that the reconstructed data is exactly identical to the source data, using a digest. Some exceptions apply. See here: Verifying file integrity.
Exceptions to Losslessness
There are some cases in which you may request
genozipto change the source data before compressing it. In these cases, the digest is not calculated. These cases are:
--optimizeor any of the
Generating Dual-coordinate VCF files with
Compressing a Luft file (a lifted-over dual-coordinates file)
Compressing a SAM or BAM file with
Compressing already-compressed files (BGZF): Many tools that generate genomic files use BGZF to compress them. These typically have a .gz extension (although not all files a .gz extension are compressed with BGZF), and BGZF compression is also used internally in .bam and .bcf files. When
genozipcompresses a BGZF-compressed file, it first decompresses it to recover the original underlying data, and then compresses the data with Genozip. Likewise, when
genounzipuncompresses a .genozip file, it recompresses the data back to BGZF if the original file was compressed with BGZF. Genozip records the parameters of the BGZF compression in the .genozip file (such as estimated compression level), and
genounzipattempts to recompress to BGZF format using the same parameters. However, since there are many BGZF compression libraries, each with dozens of parameter combinations, it is possible that
genounzipBGZF compression will achieve a slightly different compression level than the BGZF compression of the original file, resulting in the final BGZF-compressed file differing than the original BGZF file. However, the underlying data is still exactly identical and verified with the digest.
Compressing already-compressed files (.bz2 .xz and non-BGZF .gz):
genozipis capable of compressing files that are already compressed with these methods. It does so by first uncompressing the file, and then recompressing with Genozip. However, in these cases,
genounzipdoes not recompress the files back to .bz2 .xz or .gz.