15.0.42

• Removed support for Dual Coordinate VCF as well as sorting VCF files - due to very little adoption vs high maintenance cost. For DVCF, Use Genozip 15.0.41. As result, removed the command line options: --chain, --dvcf-rename, --dvcf-drop, --show-lifts, --show-chain, --show-rename-tags, --sort, --unsorted, --luft, --single-coord, --show-dvcf, --show-ostatus, --show-ref-diff, --no-kmers
• Removed experimental sex classifier (--sex option)
• BAM: better compression of files produced by Abra2
• BAM: better compression or RNA files aligned with STAR
• Faster genounzip: default BGZF compression level for outputting .gz and .bam files was changed from 6 to 1. This default may be overridden with -z.
• Windows: double-clicking on a .genozip file decompresses it

15.0.41

• speed vs compression ratio: normal mode (not --best or --fast): improve speed vs compression tradeoffs
• VCF: better compression of files generated by GATK Mutect2
• --optimize-QUAL: slight change in binning: quality score '#' remains unchanged (previously is was binned to ''')

15.0.40

• FASTQ/BAM: Better compression for some MGI Tech files
• Remove the ability to convert SAM/BAM files to FASTQ. This added a layer of complexity and did not get a lot of usage. Use genocat | samtools view -OFASTQ instead.

15.0.39

• Core engine improvements: significant reducion in RAM consumption during compression, along with modest compression gains.
• Support for Mac Apple Silicon processors in osx64 simulated mode
• Updated section 2 of the license, to grant Premium license holders the right to distribute Genozip to others.
• improved diagnostics: new options: --show-snip, --debug-tar ; --show-headers can now take either a section name or dict_id

15.0.37

• VCF: Better compression for multi-sample files where sample data is not only GT
• VCF: Better compression of GATK GVCF files
• Core engine improvements: significant reduction in RAM consumption mostly for large BAM and VCF files.

15.0.36

• BAM: Better compression of files with NanoSeq tags
• VCF: Better compression of polyploid (ploidy > 2) data
• bug fixes

15.0.35

• improvement in compression speed of very large files on systems with > 100 cores due to improved core scalability
• PacBio BAM: improved compression of subreads BAMs and unaligned CCS BAMs in some cases, particularly when using --best
• genozip --tar now also adds a copy of the genozip executables to the tar file (4 MB overhead)
• New diagnostic option: --no-zriter
• Bug fixes

genozip-15.0.34

• genozip --tar now supports compressing with --reference, see https://www.genozip.com/archiving
• New option genozip --sendto - only the designated user can decompress the file. Receiver must be a Premium user.
• New option genozip --user-message - include a message that will be displayed to users when decompressing (Premium)
• Encryption using --password is now available only in Genozip Premium
• Seamless software updates for users who installed from genozip-linux-x86_64.tar (previously available only for users who installed from conda)
• When attempting to use features allowed only for higher-level licenses, permission will be granted for evaluation
• VCF: better compression of Platypus VCF files
• New options: genocat: --analyze-insertions genozip: --prepare-for-taxid
• Canceled option: --show-flags

genozip-15.0.28

• Better compression of Ultima Genomics data: BAM/CRAM files and Deep Variant VCF files
• minor bug fixes

genozip-15.0.27

• FASTQ: compression improvements for --pair
• new option for VCF: --secure-DP. see genozip.com/genozip
• new subsetting option for SAM/BAM: --qnames - show only alignments with/without certain QNAME values
• new diagnostic tool: --show-singletons
• bug fixes