-
Notifications
You must be signed in to change notification settings - Fork 12
/
Copy pathRELEASE_NOTES.txt
1070 lines (882 loc) · 54.9 KB
/
RELEASE_NOTES.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
Note on versioning:
- Major version change occurs when the Genozip file format is extended. Note that a new Genozip version can always uncompressed files generated by an older Genozip version (Starting v15, Genozip can uncompress files generated with Genozip v11 or later. Genozip v9-v14 can uncompress files starting v8).
- Minor version changes with bug fixes and minor feature updates
- Some minor versions are skipped due to failed deployment pipelines
15.0.70 6/12/2024
- Fix issues in 15.0.69
15.0.69 3/12/2024
- 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 13/10/2024
- 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 23/9/2024
- Improvements in Deep.
15.0.66 15/9/2024
- 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 3/9/2024
- BAM: significantly reduced RAM consumption when compressing and uncompressing SAM/BAM/CRAM files in which the a large percentage 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 25/7/2024
- Bug fix: segmentation fault in Academic version (introduced 15.0.63)
15.0.63 18/7/2024
- 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 29/6/2024
- Scaling to more cores thanks to improved method of handing disk I/O
- Bug fixes
- New diagnostic options: --show-gz-uncomp, --generate-il1m
- 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
15.0.61 22/6/2024
- --optimize can now take an optional argument for fine-grained control of which fields get optimized: --optimize=QUAL,rx:f (optimize if possible, but only these fields) or --optimize=^QUAL,rx:f (optimize all fields possible, except for these fields)
- VCF: better compression of files generated by freebayes ; better compression of Type=Float annotations
- Bug fixes
15.0.60 15/6/2024
- Major revamp of the --optimize option:
> Uncompression verification for files compressed with data-modifying options --optimize, --add-line-numbers and --head: Previously, if genozip modified the original data due to these options, the correctness of the uncompression was not verified in genounzip and using --test in genozip was not possible. Now, genounzip as well as genozip --test do verify that the file is reconstructed correctly, i.e. that it is identical to the data as it was after the modifications. Note that this still does not test for any errors in the modification process itself.
> New optimization for SAM/BAM/CRAM included in --optimize: all floating point and floating point array tags (e.g. rq:f, ZP:B:f) are rounded to 10 significant bits for BAM/CRAM (i.e. an accuracy of approximately 3 siginficant decimal digits) and 3 significant digits for SAM.
> New optimization for SAM/BAM/CRAM included in --optimize: tags containing base quality scores (for example, of barcodes) are binned in the same way that QUAL is binned. The tags supported are the standard tags QT:Z CY:Z BZ:Z and the 10xGenomics/STARsolo tags UY:Z sQ:Z 2Y:Z GY:Z fq:Z QX:Z. Note that OQ:Z is not binned.
> New optimization for VCF included in --optimize: the QUAL field and all floating-point INFO and FORMAT annotations are rounded to three significant digits
> New optimization for VCF included in --optimize: GQ, SPL - Phred values are capped at 60
> quality scores in SAM/BAM/CRAM/FASTQ are not binned if they are already binned
> Command line options optimize-* --GP-to-PP --GL-to-PL are canceled - --optimize includes all the optimizations
- SAM/BAM/CRAM: Better compression of files generated by 10xGenomics CellRanger-DNA
- discontinued little-used optimization options for GFF/GVF/GTF
- discontinued little-used option --match-chrom-to-reference
- genocat --validate: change in arguments of --validate. Details: genozip.com/genocat
- bug fixes
15.0.59 29/5/2024
- CRAM is now a "first-class citizen" in Genozip - all functionality availabe for BAM is also availble for CRAM.
- SAM/BAM/CRAM: new option: genocat --cram: output a file in CRAM format
- Deep: better detection of more use cases
15.0.58 24/5/2024
- 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 21/4/2024
- 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 9/4/2024
- Bug fixes.
15.0.55 5/4/2024
- FASTQ: Support for compressing .fastq.ora files (files produced by Illumina Ora).
- VCF: Incrementally better compression of VCF
- Bug fixes
15.0.50 8/3/2024
- FASTQ: ~10% improvement in compression time and CPU consumption, without affecting compression ratio
- VCF: incremental compression improvements for GATK annotations
15.0.48 1/3/2024
- 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
- Fix bug introduced in 15.0.46 - failing to compress FASTQ files comprised of multiple concatenated gzip files.
15.0.46 21/2/2024
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 11/2/2024
- Removed support for compressing Kraken, PHYLIP and Chain files, and and all related analysis options. These files can still be compressed as generic. These were removed because they were getting very little use.
- 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 of 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 4/2/2024
- 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 1/2/2024
- 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 24/1/2024
- 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 13/1/2024
- 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 7/1/2024
- BAM: Better compression of files with NanoSeq tags
- VCF: Better compression of polyploid (ploidy > 2) data
- Bug fixes
15.0.35 30/12/2023
- 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 Premium only: 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
15.0.34 23/12/2023
- 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
15.0.28 5/12/2023
- Better compression of Ultima Genomics data: BAM/CRAM and VCF files
- minor bug fixes
15.0.27 23/11/2023
- 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
15.0.26 13/11/2023
- Incremental compression improvements for VCF
- Support for --deep for BAM files with consensus reads
- minor bug fixes
15.0.25 3/11/2023
- PacBio: further improvement of an additional 5-10% in compression of PacBio CCS and CLR files (BAM and FASTQ).
- incremental improvements in BAM and GTF compression
- Better compression of PacBio Onso short reads
- Better support of compression of .fasta.zip files (and all FASTA files compressed with ZIP)
15.0.24 23/10/2023
- BAM and VCF: verification that the contig lengths in the reference file provided with --reference match those specified in the file header
- Agilent AGeNT Trimmer: better compression of FASTQ and BAM files with Trimmer tags
- --deep now supports data in which BAM sequences may be trimmed at either end relative to their FASTQ counterparts (previously, only trimming at the end of the read was supported)
- minor bug fixes
15.0.22 15/10/2023
- BAM: better compression of BQ:Z
- Speed improvements and minor bug fixes
- Added Paid Academic license option & updated license terms accordingly
15.0.17 8/10/2023
- Bug fixes and minor compression improvements
15.0.16 29/9/2023
- FASTQ and FASTA: --multiseq option is canceled - a file consisting of sequences that are similar
to each other is now detected as such automatically, triggering the appropriate methods
- BAM: better compression of Ultima Genomics files
- bug fixes
15.0.15 12/9/2023
- Better compression of Ultima Genomics FASTQ and BAM files.
- BAM: better compression of files with a very large number of contigs (eg mapped against the transcriptome rather than the genome)
- BAM: better compression of MD:Z in files with many secondary alignments
15.0.14 29/8/2023
- new option: --no-bgzf
- bug fixes
15.0.13 19/8/2023
- VCF: Better compression of Isaac/starling files
- Recognized SAM files even if they incorrectly have an extension ".bam"
- New diagnostic option: --skip-segconf
- bug fixes
- Update of article 4 in license
15.0.12 19/7/2023
- VCF: better compression when using --reference
- genounzip of a file that was originally compressed with .bz2, .xz or .zip is now recompressed with .gz. Use --bgzf=0 to instruct genounzip to refrain from recompressing.
- bug fixes
15.0.11 18/7/2023
- FASTQ: better compression for Ultima Genomics, Singular Genomics and Element Biosciences files
- BAM: better compression for Ultima Genomics files, Isaac files
- VCF: better compression of Isaac/starling files
15.0.9 14/7/2023
- VCF compression improvements including for VEP, gnomAD, ExAC, ICGC, COSMIC, dbNSFP, Mastermind -annotated files
- FASTQ with --fast: some tradeoffs were tweaked - now it is a little bit slower but significantly better compression
- Fixed bug that affected headerless SAM (but not BAM) files when compressed with a reference file with mismatching contig names
15.0.7 5/7/2023
- Minor bug fixes
- License update: added consent to receiving product-announcement emails.
15.0.5 27/6/2023
- Minor bug fixes
- License update: clarify that hospitals of any type are excluded from academic license eligibility
15.0.4 23/6/2023 NEW MAJOR RELEASE
- Introducing Deep compression - co-compression of related BAM and FASTQ files with --deep reduces overall
compressed size by ~40%.
- Reduce compression time by ~40% on machines with > 50 cores
- GFF: support compressing GFF3 files with embedded FASTA
- BED: native support for compressing BED files - significantly better and faster compression.
- BAM: ~20% better compression for PacBio files with iq / dq / sq tags.
- VCF: better compression of dbSNP (INFO/VC field)
- VCF: better compression of DRAGEN gVCF files (FORMAT/ICNT, FORMAT/SPL)
- Reference files: redesigned reference caching - reference files generated with this release load significantly faster
(older reference files are still supported) and Genozip no longer generates or uses reference .gcache and .hcache files.
- Reference cache management: --no-cache, genols --cache
- genozip --vblock option: maximum value is now 1024 (down from 2048)
- genozip: compression with --tar now also automatically tests
- --no-upgrade (new option) disables upgrade checks
- Backward compatibility: Genozip version 15 can decompress files generated by Genozip v11 or later and can use reference files generated by v8 or later.
To decompress earlier files, used Genozip v14.
- License changes
- Many, many other compression, speed and stability improvements.
14.0.35 3/May/2023
- Bug fixes.
14.0.34 24/March/2023
- Minor bug fixes
14.0.33 15/March/2023
- Incremental improvements and minor bug fixes.
14.0.32 17/Feb/2023
- FASTQ: Fixed bug in genocat of FASTQ files compressed with --pair which sometimes caused skipping displaying
the beginning of the file. The bug was introduced in 14.0.3.
- Fixed bug with --licfile combined with --test - which incorrectly prompted for registration
- Filtering by Kraken: --taxid can now take multiple comma-separated taxonomy ids
14.0.31 14/Feb/2023
- FASTQ, BAM: incremental compression improvements
- Minor bug fixes and improvements
14.0.30 8/Feb/2023
- Minor bug fixes and improvements
14.0.29 4/Feb/2023
- Minor bug fixes and improvements
14.0.27 27/Jan/2023
- Bug fix: A bug introduced in 14.0.3 occurred when compressing FASTQ files with --pair but without --md5 and resulted
in falsely reporting that the file was verified despite not actually verifying it. This also occurred when running
genounzip or genounzip --test on such files.
There are no known issues with the actual compression of the files and it is now possible to go back and verify affected
files with (the fixed) genounzip --test.
14.0.26 25/Jan/2023
- FASTQ: Better --optimize-DESC
- Fix broken genocat --fastq (converting a SAM/BAM file to FASTQ) (broken since v14)
- Fix broken --idxstats, --coverage, --sex (broken since v14)
- Implement fix to minor htscodecs (3rd party library) bug (https://github.com/samtools/htscodecs/pull/71)
14.0.25 13/Jan/2023
- BAM, VCF: Significantly reduced memory consumption during compression
- new diagnostic option: --show-memory=PEAK - shows peak memory usage (without PEAK, shows memory at it is at the end of the execution)
14.0.24 10/Jan/2023
- Fix license enforcement bug
- Update copyright
14.0.22 8/Jan/2023
- VCF: better compression for GWAS-VCF files including support for GWAS-VCF fields in DVCF
- DVCF: better handling of some edge cases
- Change binaries in genozip-linux-x86_64.tar to be dynamically linked
14.0.21 28/Dec/2022
- Minor bug fixes
14.0.19 21/Dec/2022
- Registration flow adjustments for new website
- Change source code tree structure
14.0.18 12/Dec/2022
- GFF/GVF/GTF: Better compression ; now also supports GFF version 2 and GTF
- License: relax conditions for academic license and update sections 2,3e,5,10 for clarity ; New sections 7,8.
14.0.17 5/Dec/2022
- Website upgrade
- Better multi-threading for the case of compressing small files
- Automatic identification of file types piped into genozip (in many cases)
- Update of license term 3c
- Obsolete genounzip option --no-PG is canceled (it remains for genocat)
- VCF: Better compression of INFO/QD
- KRAKEN: new option: genozip --no-kmers - drop kmer info that is not needed for subsequent use of this file with --kraken
- Minor bug fixes
14.0.16 19/Oct/2022
- Fix bug introduced in a recent release that caused a segfault on some CPUs
14.0.14 18/Oct/2022
- License changes: sections 2, 2a, 2c, 3e, 4, 5b
- BAM: minor improvement in compression for NovoAlign-generated files
14.0.13 15/Oct/2022
- Minor improvements & bug fixes
- Change in article 3c of the license - explicitly prohibiting reverse-engineering
- New option: --submit
- New advanced option: --debug-submit
14.0.12 12/Oct/2022
- VCF: Better compression for sturctural variant fields: INFO/CIPOS and INFO/CIEND, INFO/SVTYPE
- VCF: Better compression for Illumina genotyping VCFs
- Minor bug fixes
14.0.11 5/Oct/2022
- Same as 14.0.10, just conda pipeline issues
14.0.10 5/Oct/2022
- BAM: Compression improvements for DRAGEN-created files
- BAM: better compression of UQ:i
- BAM: better support for files with a very large number (millions) of @SQ records
- Minor bug fixes
14.0.9 1/Oct/2022
- Minor bug fixes
14.0.8 28/Sep/2022
- BAM: better compression of uBAM (unaligned BAM)
- VCF: better compression of INFO/MLEAC
- Minor bug fixes
14.0.7 23/Sep/2022
- Allow kraken files to be specified as plain files in addition to genozipped files
- Minor bug fixes
- New option: --no-tip
14.0.6 23/Sep/2022
- Minor bug fixes
14.0.5 22/Sep/2022
- Allow reference files to be specified as FASTA in addition to ref.genozip
- Minor bug fixes
14.0.4 15/Sep/2022
- VCF: better compression of INFO/RAW_MQandDP, INFO/RS, INFO/RSPOS
- Minor bug fixes
14.0.3 12/Sep/2022
Summary: significant compression improvements for FASTQ, BAM, VCF in a wide range of cases. Compression and decompression are also faster.
Compression improvement:
- SAM/BAM: Better compression of Supplementary / Secondary alignments
- SAM/BAM: Better compression of SA/XA/OA, CIGAR, QNAME, MD:Z, NM:i, TLEN, MC:Z, MQ:i, ms:i, sequence, SM, AM, X0, X1, XT and other tags
- SAM/BAM: Better compression of files with methylation data created with Bismark, BS-Seeker2, Gem3, BSBolt, DRAGEN
- SAM/BAM/FASTQ: Improvements in compression of short-read QUAL.
- VCF: Significantly better compression of GVCF files
- VCF: Better compression of FORMAT/PGT, REF+ALT, QUAL, INFO, INFO/DP, FORMAT/RGQ
- FASTA: Better compression of amino acid fastas.
- Usually faster compression and decompression than previous versions
- Better license flow, upgrade notification, statistics
Command line option improvements:
- Genozip now tests after compression by decompressing the file in memory. This can be disabled with --no-test.
- SAM/BAM: genocat --FLAG now also accepts names of flags eg "--FLAG +REVCOMP". See genozip.com/bam.html.
- The --output option can now also accept a directory name - the output file is written into the specified directory, keeping its name
- BAM: BAM files created by python programs using the pysam library and which have alignments with missing quality scores (i.e. QUAL="*"), pysam encodes the missing quality in a way that violates of the SAM specification. Genozip can now handle these files regardless.
- FASTQ: Change in genocat options for FASTQ files compressed with --pair: (1) --R1 and --R2 replace the discontinued option "--component". (2) The default output format of genocat is now interleaved (up to v13, it would show the two files concatenated).
- FASTQ: Support format where read name is a number, and line3 is an SRA format
- FASTA: Much faster subsetting with --grep
- --test now defaults to verify correctness with Adler32 which is much faster than MD5. To use MD5 instead of Adler32, specifiy --md5.
- -h is now a shortcut for --header-only (previously it was a shortcut for --help)
- genounzip --bgzf=exact attempts to uncompress the file into the same BGZF compression level as the original file. Previosuly this behaviour was the default, now genounzip optimizes for speed unless "exact" is requested.
- New advanced options (see genozip.com/advanced.html for details): --log-digest, --show-sag, --show-depn, --show-lines, --show-gheader=2, --debug-read-ctxs, --debug-sag, --debug-gencomp, --no-gencomp, --no-domqual, --show-wrong-XG, --show-wrong-XM, --show-wrong-XB, --vblock with bytes specification, --show-bam, --debug-lines, --biopsy-line, --show-qual, --show-aligner, --debug-peek, --debug
Discontinued functionality:
- The little-used yet difficult to maintain feature allowing "Binding" of multiples files of the same type using eg "genozip file1.vcf file2.vcf --output bound.vcf.genozip" is no longer supported. This does NOT affect the --tar option, and also does not affect genozip files which contain two FASTQ files compressed with --pair. To compress multiple files into a single "archive" file, use "genozip --tar". To decompress existing genozip files compressed with the Binding feature, use Genozip v13.
13.0.21 21/August/2022
- Bug fix related to re-generation of reference files: compression using a reference file of 1. FASTQ files and 2. unaligned SAM/BAM files (unaligned SAM/BAM files are SAM/BAM files which have no contigs (@SQ lines) listed in their header): up to version 13.0.20, generating a Genozip reference file with "genozip --make-reference" unintentionally generated a unique reference file in each execution. It was therefore required to compress and decompress files using the same reference file,
and re-generation of the reference file from FASTA data was not possible. Starting 13.0.21 genozip --make-reference always generates the same reference file for the same FASTA data.
13.0.20 13/July/2022
- Bug fixes
13.0.19 19/June/2022
- Bug fixes
- BAM: Better support for OQ:Z
13.0.18 21/May/2022
- Bug fixes
13.0.17 18/May/2022
- Bug fixes
13.0.16 7/April/2022
- Bug fixes
13.0.15 31/March/2022
- --tar: added support for long filenames
13.0.14 29/March/2022
- Support --tar, where file uids are very large - e.g. when pulled from Active Directory using SSSD
13.0.13 25/March/2022
- Bug fixes
13.0.12 8/March/2022
- Bug fixes
13.0.11 23/Jan/2022
- VCF: Better compression of FORMAT/PS and FORMAT/PID
13.0.10 22/Jan/2022
- Bug fixes
13.0.9 21/Jan/2022
- Bug fixes
13.0.8 8/January/2022
- SAM/BAM/FASTQ: Better compression of BGI read names
- New advanced option: --debug-qname
13.0.7 2/January/2022
- SAM/BAM: bowtie2: Better compression of AS and YS fields
- Display warning if excessive dictionary size
- Fix bug where genounzip sometimes output uncompressed files when a .gz-recompression was expected
- Accept contig name "NC_012920" as equivalent to "chrM"
13.0.6 14/December/2021
- Better compression of QNAME (SAM/BAM/FASTQ/Kraken)
- Improve memory effeciency when compressing BAM integer arrays (eg B:i)
- New advanced option: --show-ref-diff - see the difference between two Genozip reference files.
- New LongR codec for quality scores introduced in 13.0.5 now used also in default mode (not just in --best as before)
13.0.5 3/December/2021
- SAM/BAM, FASTQ: Better compression of PacBio and Nanopore quality scores (in --best mode)
- VCF: Better compression for FORMAT/PS, FORMAT/GT, FORMAT/GQ, INFO/DP
- Illumina formats: Better compression for .locs files
- --multiseq (renamed from --multifasta) now works on FASTQ files too, in addition to FASTA
13.0.4 19/November/2021
- Better support for EasyBuild installations - see https://genozip.com/using-on-hpc.html
- new option: --subdirs to recursively compress subdirectories
- SAM/BAM: Better compression of CP:i
- Performance enhancements
13.0.3 15/November/2021
- VCF: better compression of FORMAT/GL in --best
- DVCF: more granular statuses, canceled --ext-ostatus
- CRAM: now compresses as BAM instead of SAM
13.0.2 8/November/2021
- Native (binary) handling of BAM integers --> faster compression, up to 2X faster in BAM files with long arrays (eg PacBio subreads, IonTorrent)
- Advanced option: --biopsy
13.0.1 4/November/2021
- Significant speed improvement in compression and decompression due to faster dict_id->did_i mapping, elimination of
thread synchronization bottlenecks and integration of fast htscodecs.
- Faster --fast mode, and better --best mode
- SAM/BAM compression improvements: Better compression of MAPQ, MQ:i, XS:i, TLEN, CIGAR, ms:i (biobambam)
- VCF compression improvements: better compression for sample fields GL,PP,PL,PRI,GP,DS,AD and files generated by VarScan.
- VCF: Liftover fidelity improvements in DVCF
- VCF: genocat --indels-only now also excludes variants which have an INFO/SVTYPE field
- FASTA compression improvements: Better compression of amino acid sequences
- GFF/GFF3: Support more variations of the format, including output of Maker and GFF (not only GFF3) output of Ensembl
- Accept human contig names eg NC_000001.10 as equivalent to 1 or chr1 (and similarly for human chromosomes 1-22,X,Y)
- Rename advanced option --debug-allthesame -> --debug-generate
- Advanced option: --show-containers can now accept an argument for additional output
- Much faster --make-reference
12.0.42 13/October/2021
- SAM/BAM: better compression for Z5:i, XM:i
- bug fixes
12.0.41 12/October/2021
- SAM/BAM: significantly better compression for sorted (by POS) files
12.0.37 28/September/2021
- SAM/BAM: better NM:i, MD:Z, MQ:i, QNAME compression
- FASTQ: --optimize-DESC now generates read names similar to the NCBI format, eg "@sample.6"
- New advanced option: --show-wrong-md
12.0.36 24/September/2021
- New: genozip --match-chrom-to-reference: rewrite contig names to match the provided reference file (eg "22"->"chr22"), see https://genozip/match-chrom.html
- Chain files can now be subsetted with --regions
- More accurate progress indicator
- Better support for contigs named by accession number, eg "GL000192.1", "chrUn_JTFH01001867v2_decoy", "chr4_gl383528_alt"
- New advanced option: --debug-seg
- Advanced option --show-ref-alts renamed --show-chrom2ref
- faster --downsample when used with very large values
- Relax section 2f of the license
- Removed obsolete --with-chr
- Bug fixes
12.0.34 9/September/2021
- Compile without -march=native for genozip-linux-x86_64 and Windows Installer distributions
- Better support for IUPAC "bases" in reference files
- DVCF: detect many-to-one coordinate mapping and generate an .overlaps file
- VCF: better INFO/ANN, INFO/CLNHGVS, INFO/CSQ compression
- SAM/BAM/FASTQ/FASTA/Kraken: better compression of QNAME / Description
- SAM/BAM: Faster compression and decompression of SA, OA, XA with long reads
- Faster --test
- More robust compression from a URL, even on flakey connections
- Improved --STATS report
- bug fixes
12.0.33 31/August/2021
- Fix backward compatibility issue of decompressing FASTQ files compressed with --pair in v9.0.12 or earlier
- FASTQ: genocat --seq-only and genocat --qual-only: output only the Sequence / Quality lines
- DVCF: genocat --single-coord : Generates single-coordinate ("normal") VCF. Can be used with or without --luft
- DVCF: genocat --contigs --luft: show the contigs of the Luft coordinate
- FASTA: support --make-reference when contigs in FASTA are sequential (i.e. not broken into short lines)
- SAM/BAM/FASTQ/FASTA/Kraken: better compression of QNAME / Description
- SAM/BAM/FASTQ: Faster compression of long reads
- bug fixes
12.0.32 26/August/2021
- Faster loading of reference files
12.0.31 23/August/2021
- Better GFF3 compression
- Many minor bug fixes and cosmetics
12.0.30 15/August/2021
- Extended the genocat --fastq option for converting SAM/BAM to FASTQ: now --fastq=all emits all the SAM/BAM fields in the FASTQ description lines.
12.0.26 13/August/2021
- FASTA improvements: compression improvement for amino acid FASTAs; support --downsample ; support .fas and .frn filename extensions
12.0.25 9/August/2021
- DVCF: added tag renaming ; RengAlg attribute of ##INFO and ##FORMAT now enclosed in quotes.
- VCF: better compression for INFO/CLNDN, INFO/CLNHGVS, INFO/RS, INFO/ALLELEID
- When loading implicit reference files with a relative path, first try path relative to current directory, and then relative to file's directory.
12.0.14 29/July/2021
- FASTQ: support files where the 3rd line is a copy of the 1st line, except with '+' prefix instead of '@'
- DVCF: a. lift-over of complex indels ; b. consistent sorting of lines that have the same CHROM/POS c. alt chrom names also if VCF has no contigs in header
- snips with len > 512K (technical improvement)
12.0.13
- Option change: --grep for fastq now tests the entire read, not just the description
- Option change: --interleaved now has an optional paramter --interleave=either or --interleave=both (default: both) describing how to handle in case of subsetting with eg --grep
12.0.12 24/July/2021
- Better support for compressing gff3 files
12.0.10 + 12.0.11 22/July/2021
- bug fixes
12.0.7 + 12.0.8 16/July/2021
- license and copyright update
12.0.6 15/July/2021
- new option: --tar to archive with genozip. See: https://genozip.com/archiving.html
- new option: --files-from/-T - An alternative to providing input file names on the command line
- bug fixes
12.0.5 9/July/2021
- Compressing low-coverage SAM/BAM files without a reference: better compression ratio, better decompression performance
12.0.4 8/July/2021
- safer implementation of --replace
- updated non-commercial license
- bug fixes
12.0.3 6/July/2021
- new option: --licfile. See genozip.com/using-on-hpc.html
12.0.2 2/July/2021
a. Dual-coordinate VCF files: genozip --chain to create a dual-coordinates file ; genocat --luft ("lifted") to see https://genozip.com/dvcf.html
b. Filtering by taxonomy using kraken2 files - support for compressing kraken output files --kraken, --taxid, see: https://genozip.com/kraken.html.
c. Many other improvements:
- Support genocat --sort for VCF files ; --sort implied for dual-coordinates VCF files. Disabled by --unsorted.
- Fixed bug with subsetting samples in VCF (genocat --sample). The fix will work on files compressed with 11.0.9 onwards.
- Now, genounzip always unbinds files, and genocat always concatenates
d. New options:
- new option: genocat --component <component-number> - to view a single component of a bound file (including one of the fastq files in a paired file)
- new option: genocat --lines [start]-[last] - show a subset of lines of the file.
- new option: genocat --head [num_lines] - show lines from the start of the file.
- new option: genocat --tail [num_lines] - show lines from the end of the file.
- new option: genocat --count - displays the number of lines (or reads in the case of FASTQ), that
survived any filters applied (--regions, --grep, --taxid, --FLAGS, --MAPQ, --bases, --component, --one-vb etc)
- new option: --show-filename - Show the file name for each file
- new option: genocat --FLAG - filters a SAM or BAM file by the value of the FLAG field
- new option: genocat --MAPQ - filters a SAM or BAM file by the value of the MAPQ field
- new option: genocat --bases - filters a SAM/BAM/FASTQ for SEQ base values
- new option: --echo displays the command line and a timestamp upon completion ofq execution (successful or failed)
- new option: genocat --regions-file - reading regions from as an alternative to --regions
- new option: genocat --show-chain - for chain files - show chain file alignments
- new option: genocat --show-chain-contigs - for chain files - show contig list
- new option: genocat --with-chr - for chain files - changes eg 22->chr22 and MT->chrM for all qNames
- discontinued support for GTShark codec - use genozip v11 to decompress old VCF files compressed with --gtshark
- VCF: better compression of FORMAT/F2R1, INFO/MLEAC, INFO/AA, FORMAT/MB, FORMAT/SB, FORMAT/ADALL, FORMAT/ADF, FORMAT/ADR, FORMAT/AF, FORMAT/SAC
e. Option changes:
- genozip - resturctured optimization options for VCF: --optimize-phred, --GL-to-PL, --GP-to-PP
- genounzip now always unbinds files, and the --unbind is canceled. the --prefix can now used to set a prefix.
- genocat --fastq will NOT add /1 or /2 to R1 and R2 reads in the case that --FLAG is specified as well
- genocat --grep now works with most data types, --grep-w restrict to whole words
- genocat --samples now also accepts a number - "--samples 5" shows the first 5 samples
- genocat --validate=valid displays filenames that are valid genozip files. No change when used without "=valid".
- genols --unbind (-u) option is renamed --list (-l). genozip --list option is canceled.
- --sex, --coverage, --stats and --STATS replace --show-sex, --show-coverage --show-stats, --SHOW-STATS respectively
- --chroms, and --contigs are accepted as alternative names for --list-chroms
- Setting the environment variable GENOZIP_REFERENCE is now equivalent to --reference
- Default number of threads is now 75% of cores for Windows and Mac and 110% of cores for Linux (modifiable with --threads)
f. New advanced options:
- new option: genocat --show-dvcf - shows line-by-line result of the liftover (applied to a dual coordinate VCF file)
- new option: genozip --show- n - used in combination with --taxid
- new option: --show-uncompress. Shows uncompressing of section data.
- new option: --show-flags. Shows internal flags after initialization.
- new option: --show-plan. Shows reconstruction plan
- new option: --show-ref-iupacs. Show non-ACGT iupac codes in a reference file
- new option: --debug-stats. For debugging development of stats.c
- new option: --debug-allthesame. For debugging development of the allthesame algorithm
- new option: --show-buddy. For debugging SAM/BAM buddy method
g. Much improved website genozip.com
11.0.11 24/March/2021
- Fix bug with concatenating multiple files with genocat
- genocat <file1> <file2>.... now will show the header of only the first file. To show headers of all files use
genounzip --stdout instead.
11.0.9 20/March/2021
- Fix bug with --downsample in combination with --interleaved
11.0.8 9/March/2021
- Added sharding with genocat --downsample <rate>,<shard>
- Added support for compressing UCSC chain files
- Better --show-coverage
- Bug fixes
11.0.7 5/March/2021
- Added genozip --idxstats - identical output to samtools idxstats
- Much improved genocat --show-sex and --show-coverage
- Bug fixes
11.0.6 2/March/2021
- Added genocat --show-coverage and --show-coverage-chrom
- Added "Male-XXY" result to genocat --show-sex
- Added genocat --validate
- Better hash table sizing algorithm - reduced memory consumption
- Developer tools: Added <bytes> option to --debug-memory[=bytes]
- Developer: add kill -USR1 - --show-memory of a running process
- Bug fixes
11.0.5 27/Feb/2021
- Added genocat --show-sex for sex assignment of a SAM/BAM file
- Improve Windows installer
- Windows: add genozip directory to Path in registry, if not already there
- Bug fixes
11.0.4 20/Feb/2021
- bug fixes
11.0.3 20/Feb/2021
- Added registration requirement to the non-commerical license (2.d.)
- Bug fixes
- windows installer relocated from windows/ to docs/
11.0.2 13/Feb/2021
- Bug fixes
11.0.0 11/Feb/2021
- VCF: introduce a PBWT based codec for compression of the haplotype matrix. Retire hapmat and gtshark codecs.
backward compatibility is provided for decompressing VCF files compressed in earlier versions of genozip with hapmat or gtshark
- SAM: better handling of optional fields SA, OA, XA
- Better memory management in Linux
- Reduce core oversubscription from 1.4 to 1.2
- Add --multifasta option for better compression of a FASTA where the contigs are quite similar to each other
10.0.9 11/Jan/2021
- bug fixes
10.0.8 10/Jan/2021
- VCF: better handling of INFO/SF
10.0.5 8/Jan/2021
- VCF: better handling of FORMAT fields DP, AD, ADF, ADR, AD_ALL, PL and INFO fields DP, BaseCounts
10.0.4 8/Jan/2021
- VCF: better handling of FORMAT/DS
- Bug fixes
10.0.3 7/Jan/2021
- Better --gtshark mode for VCF
10.0.2 7/Jan/2021
- Better memory usage in ZIP (canceled Context.node_i)
- Better handling of VCF haplotype matrices with hetreogeneous ploidy
- Bug fixes
10.0.0 31/Dec/2020
- Increased MAX_FIELDS from 64 to 2048. This sets the maximum number of INFO and FORMAT tags in VCF,
maximum number of optional fields in SAM/BAM and maximum ATTR in GVF.
- Set size of vblock dynamically
- VCF: support FORMAT tags that begin with a character other than a letter (eg a digit)
- VCF: better handling of INFO arrays
- VCF: better handling of VEP fields: CSQ, DP_HIST, GQ_HIST, AGE_HISTOGRAM_HET, AGE_HISTOGRAM_HOM
- VCF: better handling of FORMAT/DP and FORMAT/GQ - transposed matrix
- Several other bug fixes
- Backward compatible with Genozip 8 and 9 - v8 and v9-compressed files can be read by v10
9.0.22 28/Dec/2020
- more consistent --bgzf, --sam, --bam behavior in genocat
- better --stats
- minor bug fixes
9.0.21
bug fixes, including major bug with mc:i optional field in SAM
9.0.20 27/Dec/2020
- allow --output to a named pipe (fifo) (not available on Windows)
- genounzip --bgzf now requires a level parameter (0 to 12). 0 means no compression, and hence --plain flag is canceled.
- bug fixes
9.0.17 20/Dec/2020
- refactor access to the reference file - to using memory mapping and cache files - a lot faster and consumes less memory
- when compressing a .gz (or BAM), test BGZF blocks against zlib too (with all compression levels), in addition to libdeflate
- append /1 and /2 to the qname in fastq files in both --interleave of a paired fastq file and --fastq of a sam/bam file
- renamed --test-seg to --seg-only
- bug fixes
9.0.15 14/Dec/2020
- bug fixes and minor improvements
9.0.14 12/Dec/2020
- added better selection of stdout vs stderr for messages (info_stream)
- bug fixes
9.0.13 10/Dec/2020
- added genocat --interleave: displays pairs of FASTQ files compressed with --pair with their reads interleaved.
9.0.12 8/Dec/2020
- bug fix
9.0.11 7/Dec/2020
- Fixed critical bug introduced in 9.0.0 in which FASTQ files that were compressed with BGZF (i.e. fq.gz),
and genozipped with --pair, did not compress correctly
- Added Phylip data type
- genozip --pair can now compress any number of fastq files - every 2 consecutive files are considered a pair
- genocat --header-one now works of FASTA too: Output the sequence name up to the first space or tab
- genocat --phylip new translator - outputs a multi-fasta file in Phylip format
- genocat --fasta new translator - outputs a Phylip file in multi-fasta format
- bug fixes
- Developer options:
--xthreads Use only 1 thread for the main PIZ/ZIP dispatcher. This doesn't affect thread use of other dispatchers
--show-headers now accepts a section-type as an optional argument
9.0.10 2/Dec/2020
- Added the --index option for genounzip / genocat to create an index file alongside the decompressed file
9.0.8-9 2/Dec/2020
- bug fixes
9.0.7 1/Dec/2020
- New flags:
genocat --downsample <rate> - show only one in every X lines (or reads)
genocat --one-vb <vb> - show data from a single VB
- bug fixes
9.0.1-6 1/Dec/2020
- bug fixes and minor improvements
9.0.0 29/Nov/2020
Functionality:
- Native compression of BAM (no longer using samtools for BAM)
- Native reading and writing of BGZF data
- New data type: "generic" for compressing any file beyond our supported genomic formats
- Framework supports file translations SAM->BAM, BAM->SAM, SAM/BAM->FASTQ, 23andM3->VCF
- Framework supports binary source files
- Backwards compatible with v8 - v8-compressed files can be read by v9
- When decompressing a file that was originally compressed with BGZF (eg BAM, fq.gz...) - the BGZF blocks are reconstructed,
with an attempt to guess the original compression level
- File is now always verified - if md5 is not selected, then Adler32 is used
- New / changed flags:
--sam (new flag) for genounzip/genocat - reconstruct a SAM/BAM file as SAM
--bam (new flag) for genounzip/genocat - reconstruct a SAM/BAM file as BAM
--no-PG (new flag) refrain from adding a @PG record to the header when converting SAM->BAM or BAM->SAM
--fastq (new flag) for genounzip/genocat - reconstruct a SAM/BAM file as FASTQ
--vcf (new flag) genounzip/genocat - reconstruct a 23andMe file as a VCF
--plain (new flag) in genounzip / genocat - negates implicit --bgzf
--dump-local and --dump-b250 (renamed from dump-one-local and dump-one-b250) now output a file per VB
--bytes (new flag) for genols - show sizes in bytes
--dump-section (new flag)
--show-bgzf (new flag) for genozip - show bgzf blocks
--show-containers (new flag) for genounzip/genocat - show flow of container reconstruction
--show-time can now accept an optional argument eg. --show-time=compressor
--show-txt-contigs - shows contigs from the SAM/BAM header (SQ lines)
--show-mutex - shows locks and unlocks of a particular mutex
--unbind in genols (new flag) - shows the components of bound files
--show-dict and show-b250 now accept an optional paramter + removed --show-one-dict and --show-one-b250
--show-digest show (md5 or Adler32) updates
--stdout - flag canceled for compression (genozip), available for decompression (genounzip, genocat, genozip -d)
--input - renamed from --input-type
Compression improvements:
- For b250 sections that have all the same entry - store the entry only once. If the entry is word_index=0, drop the section
- Improvements in codec assignment algorithm, and use it for dictionary and some other section types in addition to b250 and local
- 30% improvment in dictionary size of disk due to consolidation of fragments and codec assignment.
- Multi-threaded decompression of dictionaries.
- Speed improvements by having bsc and zlib use libdeflate's version of adler32 and crc32
Cleanup:
- removed support for Visual C compiler
8.0.4 8/Nov/2020
- 10X improvement in --gtshark speed by moving to in-memory comms using fifo
- fix thread safety issue in bits.c
8.0.3 23/Oct/2020
- Support samtools with or without --no-PG
- Fix reading and writing BAM files using samtools
- Fix bug in genocat --show-headers
- Add back gtshark as a codec for VCF allele data, --gtshark option
8.0.2 20/Oct/2020
- Bug fixes
- Improved 'genocat --show-headers'
8.0.0 16/Oct/2020
- Added libbsc codec
- Dynamic selection of codec between lzma, bz2, bsc for each local and b250 buffer
- --show-ref-seq can now work in combination with --regions in genocat/genounzip
- Better license registration flow
- Consume ~0.5GB (for human data) less RAM in genounzip of SAM files compressed without a reference
- In --regions, allow specification or ranges using length eg "chr22:1000+151" - equivalent to "chr22:1000-1150"
- Canceled optimize-SEQ (benefits were tiny if any, but it slowed down --optimize considerably)
- Added --best to contrast --fast. --best doesn't have any additional effect as its the default mode of genozip.
- Added =prefix option to --unbind, to add a prefix when unbinding
- --reference in genounzip is now optional - will use original reference filename absent --reference
- Not backward compatible
7.0.5 10/Oct/2020
- Add --show-stats and --SHOW-STATS to genocat/genounzip by introducing a new section SEC_STATS ; remove limitation of only one file when -w or -W
7.0.4 4/Oct/2020
- Bug fixes
7.0.3 3/Oct/2020
- Bug fixes
7.0.2 2/Oct/2020
- Even better SAM BD/BI codec
7.0.1 29/Sep/2020
- bug fixes
- new --test-seg debug option
- change default number of threads to 1.4 * number of cores
7.0.0 28/Sep/2020
- Re-write the VCF segmenter to use the modern infrastructure of recursive data definition. In the process, some little-used
features were discontinued: --gtshark, --sblocks. Non-GT subfields are now compressed as is (not transposed), and each
field on its own. Samples as well as the GT field are defined as Structured.
- Removed gloptimization - too small of a benefit for non-standard code
- Change all data types to be fully recursive starting at TOPLEVEL, removing data-type specific reconstruction loop
- Added caching of Structured in PIZ
- Better BD and BI compression for SAM
- Not backward compatible
- Bug fixes
6.0.11 21/Aug/2020
- Bug fixes
6.0.3 19/Aug/2020
- Added new data type for reference files - and an option for creating a reference file from a FASTA - --make-reference
- Added compression against reference for FASTQ, SAM and VCF - new options --reference and --REFERENCE
- Added --pair to compresses pairs of paired-end fastq files together, resulting in significantly better compression
- Added Domqual compression method, for handling dominant quality scores such as Illumina binned quality scores in FASTQ and SAM
- Added ACGT compression codec for nucleotide sequences
- Added support for compressing CRAM files
- Added better compression for FORMAT/PS, INFO/AC, INFO/AF, INFO/AN, INFO/SVLEN in VCF
- Added --optimize-DESC for FASTQ optimization
- Added --optimize-SEQ for FASTQ, FASTA, SAM optimization
- Added many options including --list-chroms, --dump-one-local, --show-reference, --show-ref-index, --show-ref-seq, --show-chrom2ref,
--show-ref-contigs, --show-ref-hash
- Removed backward compatability with versions v1 and v5. Use genozip version 5 to decompress files of all previous versions.
5.0.9 16/June/2020
- fix bug with compressing VCF / GVF with an INFO / ATTRS field of '.'
5.0.7 2/June/2020
- bug fixes
5.0.5 31/May/2020
- Updated license
- Added user registration
- Added full support for compressing SAM/BAM, FASTQ, FASTA, GVF and 23andMe files
- Compression improvements for VCF files with any of these:
1. lots of non-GT FORMAT subfields
2. ID data
3. END INFO subfield
4. MIN_DP FORMAT subfield
- Added genounzip output options: --bcf for VCF files and --bam for SAM files
- Added --input-type - tell genozip what type of file this is - if re-directing or file has non-standard extension
- Added --stdin-size - tell genozip the size of a redirected input file, for faster execution
- Added --show-index for genounzip and genocat - see index embedded in a genozip file
- Added --fast option for (a lot) faster compression, with (somewhat) reduced compression ratio
- Added --grep for genocat FASTQ
- Added --debug-progress and --show-hash, useful mostly for genozip developers
- Reduce default vblock from 128MB to 16MB
- Cancel option --strip
list
Note: some versions numbers are skipped due to failed conda builds (every build attempt consumes a version number)
4.0.11 30/March/2020
- bug fixes
4.0.10 28/March/2020
- updated license
- added --header-one to genocat
- query user whether to overwrite an existing file
- better error messages when running external tools
- bug fixes
4.0.9 27/March/2020
- improve performance for --samples --drop-genotypes --gt-only --strip and --regions - skip reading and decompressing
all unneeded sections (previously partially implemented, now complete)
- bug fixes
4.0.6 25/March/2020
- bug fixes
4.0.4 24/March/2020
- add support for compressing a file directly from a URL
- remove support for 32-bit Windows (its been broken for a while)
4.0.2 23/March/2020
- genozip can now compress .bcf .bcf.gz .bcf.bgz and .xz files
- genounzip can now de-compress into a bgzip-ed .vcf.gz file
4.0.0 21/March/2020
- a bug that existed in versions 2.x.x and 3.x.x, related to an edge case in compression of INFO subfields.
fixing the bug resulted in the corrected intended file format that is slightly different than that used in v2/3.
Because of this file format change, we are increasing the major version number. Backward compatibility is provided
for correctly decompressing all files compressed with v2/3.
- VCF files that contain lines with Windows-style line ending \r\n will now compress losslessly preserving the line
ending
3.0.12 20/March/2020
- added genocat --GT-only
3.0.11 20/March/2020
- added genocat --strip
3.0.9 19/March/2020
- bug fixes