genozip-15.0.71

Minor updates

15.0.70

• Fix issues in 15.0.69

15.0.69

• New major feature: --bamass : BAM-assisted compression of FASTQ files
• FASTQ and BAM: Speed and RAM consumption improvements
• VCF: support unlimited number of ALT alleles per variant (previously limited to 99)
• VCF: better compression for files with a large number of samples and gVCFs
• License updated to reflect introduction of Biobank, Research and Student licenses
• bug fixes

15.0.68

• Deep: reduction in memory in --test and genounzip of Deep files: typically 10-20% less RAM consumption
• Deep: new option: --deep=no-qual to Deep seq, qname only (not qual): consumes drastically less RAM, and generates a file of size in between compressing the FASTQ and BAM alone, and full Deep.
• License: clarify the meaning of "Recognized Academic Research Institution"
• BAM: further reduction in RAM consumption when compressing and uncompressing files with many secondary or supplementary alignments.
• New diagnostic: --show-huffman

15.0.67

• Improvements in Deep.

15.0.66

• BAM: better compression of PacBio and Nanopore files generated with minimap2, pbmm2, winnowmap
• BAM: further small reduction in RAM consumption when compressing and uncompressing SAM/BAM/CRAM files with many Supplementary and Secondary alignments
• Bug fixes

15.0.65

• BAM: significantly reduced memory consumption when compressing and uncompressing SAM/BAM/CRAM files in which the majority of alignments are secondary alignments.
• BAM: better compression for files genereated by CPU (https://github.com/cheehongsg/CPU)
• New diagnostic options: --show-sec-gencomp, --show-reading-list, --force-reread, --show-scan
• Bug fixes

15.0.64

• Bug fix: segmentation fault in Academic version (introduced 15.0.63)

15.0.63

• FASTQ: much faster compression of most MGI, most Element, and some Illumina FASTQs due to better scaling of CPU cores on machines with > 40 cores
• New option: --not-paired: used in combination of --deep to inform Genozip that the two FASTQs files provided are not paired-end.
• Bug fix: correct handling of BGZF-compressed files with a BGZF End-of-File block in their midst (instead of at their end): Until version 15.0.46 the file was compressed up the BGZF EOF block, and the rest of the file was lost. Between 15.0.48 to 15.0.62 Genozip errored on this situation. This edge case was discovered during development and has not been encountered so far in any real-world files.

15.0.62

• I/O optimizations for faster compression
• Bug fixes
• New diagnostic options: --show-gz-uncomp, --generate-gzil
• Removed bash autocomplete for genozip as it didn't work very well. If this was installed, it can be removed by manually editing ~/.bash_completion