15.0.58

• FASTA: New method (FAF) for better compressing FASTA files that contain sequencer reads (as opposed to assembled contigs), including support for --reference
• FASTA: genozip option --index now required in order to enable genocat --grep and --regions on files with more than 10,000 contigs (flles with less contigs are indexed by default)
• FASTQ/FASTA: better compression of interleaved data
• SAM/BAM: better compression of files containing OQ:Z
• VCF: better compression of files containing Mobile Elements data, and files generated by Illumina Starling
• bash: autocomplete of files and command line options in bash. .bashrc is modified during registration to activate the autocompletion. For existing users, you may manually add the following line to your .bashrc :
  source <...genozip-directory...>/autocomplete.sh ; complete -F _genozip genozip; complete -F _genounzip genounzip ; complete -F _genocat genocat ; complete -F _genols genols
• feature matrix changes: --optimize is now available only in Genozip Enterprise, Premium and Academic (not Genozip Standard) (no change for current Genozip Standard customers)
• some command line options renamed: --show-reference, --show-ref-contigs, show-ref-iupacs and --show-filename have been renamed to --print-reference, --print-ref-contigs, print-ref-iupacs and --print-filename respectively. The old names still work too, for backward compatability.
• new diagnostic options: --no-FAF and --no-interleaved to disable the FAF and Interleaved methods respectively ; --debug-upgrade

15.0.57

• genounzip/genocat: GENOZIP_REFERENCE environment variable can now accept either a file name
  (of the reference file) OR the directory where it is located (the latter is new).
• Support for Mac with Apple Silicon (requires MacOS version 13 or higher)
• Fix bug introduced in 15.0.55: compressing with --test tested only partially. You may use genounzip --test to test previously compressed files.
• Fixed bug causing errors on old Macs

15.0.56

• Bug fixes

15.0.55

• FASTQ: Support for compressing .fastq.ora files (files produced by Illumina Ora).
• VCF: Incrementally better compression of VCF
• Bug fixes

15.0.50

• FASTQ: ~10% improvement in compression time and CPU consumption, without affecting compression ratio
• VCF: incremental compression improvements for GATK annotations

15.0.48

• VCF: better compression of structural variants
• Support for compressing FASTA files with descriptions lines starting with @ instead of > (as generated by NCBI)
• Small speed gains
• New diagnostic option: --show-stack
• Bug fixes

15.0.46

This release is all about speed:

• genozip FASTQ: up to 1.7X-2X faster compression for most (but not all) FASTQ files without affecting the compression ratio
  due to a combination of better core scalability and various optimizations.
• genounzip FASTQ/BAM/VCF: 1.5X faster decompression to disk (i.e. not in --test mode)
• change in genounzip/genocat --bgzf (-z) parameter: range is now from 0 (no compression) to 5 (maximum compression)
• genocat --bgzf=exact now works also when decompressing a single file from a co-compressed .genozip file (i.e. compressed with --deep or --pair)
• new diagnostic option: --show-gz (see: genozip.com/losslessness)

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.