15.0.69

.gitattributes

@@ -1,50 +1,50 @@
-# Set the default behavior, in case people don't have core.autocrlf set.
-* text=lf
-
-*.sh eol=lf
-*.txt eol=lf
-*.md eol=lf
-*.eb eol=lf
-*.json eol=lf
-*.sed eol=lf
-*.c eol=lf
-*.cpp eol=lf
-*.h eol=lf
-*.asm eol=lf
-*.S eol=lf
-*.yaml eol=lf
-Makefile eol=lf
-
-# Declare our textual formats as binary so we can check in test files with Unix or Windows style end-of-lines
-*.vcf binary
-*.bcf binary
-*.sam binary
-*.bam binary
-*.cram binary
-*.gff3 binary
-*.gff binary
-*.gvf binary
-*.gtf binary
-genome_*.txt binary
-*.fa binary
-*.fasta binary
-*.fa binary
-*.faa binary
-*.ffn binary
-*.fnn binary
-*.fna binary
-*.frn binary
-*.fas binary
-*.fq binary
-*.fastq binary
-*.phy binary
-*.bed binary
-*.kraken binary
-*.chain binary
-*.locs binary
-*.genozip binary
-
-# installer files
-*.tar binary
-*.exe binary
-*.o binary
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=lf
+
+*.sh eol=lf
+*.txt eol=lf
+*.md eol=lf
+*.eb eol=lf
+*.json eol=lf
+*.sed eol=lf
+*.c eol=lf
+*.cpp eol=lf
+*.h eol=lf
+*.asm eol=lf
+*.S eol=lf
+*.yaml eol=lf
+Makefile eol=lf
+
+# Declare our textual formats as binary so we can check in test files with Unix or Windows style end-of-lines
+*.vcf binary
+*.bcf binary
+*.sam binary
+*.bam binary
+*.cram binary
+*.gff3 binary
+*.gff binary
+*.gvf binary
+*.gtf binary
+genome_*.txt binary
+*.fa binary
+*.fasta binary
+*.fa binary
+*.faa binary
+*.ffn binary
+*.fnn binary
+*.fna binary
+*.frn binary
+*.fas binary
+*.fq binary
+*.fastq binary
+*.phy binary
+*.bed binary
+*.kraken binary
+*.chain binary
+*.locs binary
+*.genozip binary
+
+# installer files
+*.tar binary
+*.exe binary
+*.o binary

LICENSE.txt

@@ -30,10 +30,13 @@ original work of authorship. For the purposes of this License, Derivative Works
 works that remain separable from Genozip and Derivative Works thereof.
 
 "Your Commercial Data" shall mean data which You (the Legal Entity exercising permissions granted
-by this License) obtained with intention of using it in the development process of a product and/or
-for provisioning of any kind of service (including also clinical, diagnostic, DNA or RNA
-sequencing, bioinformatics and cloud services, but excluding education services) for which You get
-paid. Data derived from Your Commercial Data is also Your Commerical Data.
+by this License) obtained with intention of using it in the development process of a product or
+service and/or was obtained and/or will be used in the context of any kind of service You provide 
+(including also: sequencing, bioinformatics, diagnostic, clinical, research-on-contract, IT,
+product development, inspection, biobanks and other dataset aggregations for consumption by
+external users (even if for academic purposes).) for which You get paid, including through fees,
+grants, salary or government funding. Data derived from Your Commercial Data is also Your
+Commerical Data.
 
 "Your Computers" shall mean computers You own and/or cloud accounts You own at 3rd party cloud
 providers.
@@ -50,20 +53,21 @@ you meet the conditions attached to any of the License Types a through f below,
 purpose attached to that particular License Type, and subject to the terms and conditions of this
 License agreement:
 
-   a. Academic License: Using Genozip Executables for academic research, educational or training
-purposes provided that You are a Recognized Academic Research Institution which is not a hospital,
-or a registered student at such an institution, but excluding use with Your Commercial Data, and
-limited to a total of 10,000 files per institution.
+   a. Research License: Using Genozip Executables for academic research, educational or training
+purposes provided that You are a Recognized Academic Research Institution which is not a hospital
+but excluding use with Your Commercial Data, and limited to a single lab or project within a single
+institution.
 
-   b. Academic License: Using Genozip Executables for another non-commercial purpose, if it has
-been pre-approved by Licensor in writing. Email [email protected] to seek such an approval.
+   b. Student License: You are a student enrolled in an academic degree program in a Recognized
+Academic Research Institution, and your use of Genozip is related to your studies.
 
    c. Standard, Enterprise or Premium License: Using Genozip Executables for any legal purpose, if
 the license was purchased and paid for, and for the duration that it is in effect. In addition, for
 Premium License only: Distributing Genozip Executables to others.
 
    d. Decompression License: Using a subset of Genozip Executables consisting of genounzip,
-genocat, genols for any legal purpose. A Decompression License is free of charge.
+genocat, genols for any legal purpose, on files that were compressed with a valid Genozip license.
+A Decompression License is free of charge.
 
    e. Evaluation License: Using Genozip Executables for the purpose of evaluating Genozip, free of
 charge, for a duration of 30 days, if You were not already granted an Evaluation License in the
@@ -73,7 +77,11 @@ past. The duration of an Evaluation License may be extended by written email app
 platform that is free of charge, including (but not limited to) an Internet website, a package or
 container management system, or a module on an institutional HPC. A Distribution License is free of
 charge. Each end user must independently register to Genozip and be granted a Standard, Enterprise,
-Premium, Academic, Decompression or Evaluation License.
+Premium, Research, Student, Decompression or Evaluation License.
+
+   g. Biobank License: Using Genozip Executables to compress data for a public or cross
+-institutional genomic data repository by certain users named on the license, if the license was
+purchased and paid for, and for the duration that it is in effect.
 
 3. Additional Terms and conditions
 
@@ -100,18 +108,19 @@ Genozip's code or algorithms (together, "Genozip Technology") such that a user o
 product may directly or indirectly effectuate compression or decompression of data using Genozip
 Technology - permission for such reselling or selling is not granted in this license, and requires
 a separate reseller or OEM license. To clarify, merely delivering Genozip-compressed files to
-others (e.g. your clients or collaborators) IS included in the Standard, Enterprise, Premium and/or
-Academic License and IS NOT subject to this restriction.
+others (e.g. your clients or collaborators) IS included in the Standard, Enterprise, Premium,
+Research and/or Student License and IS NOT subject to this restriction.
 
 4. Severely Unauthorized Use of Genozip. Use which is either: a. with no license (Standard License,
-Enterprise License, Premium License, Acedemic License, Evaluation License, Decompression License or
-Distribution License) granted according to section 2; and/or b. non-compliant with any of sections
-3a, 3c, 3e; and/or c. use of Genozip for which you were granted an Academic License to compress
-Your Commercial Data - shall be considered Severely Unauthorized Use of Genozip. In this case, You
-agree to a. pay Licensor US$100.00 for each file You compressed with Genozip b. that Licensor shall
-be eligible for 20% ownership of any revenue generated and intellectual property created that
-involved the Severely Unauthorized Use of Genozip. c. reimburse licensor for all legal and/or
-collection costs related to Your Severely Unauthorized Use of Genozip.
+Enterprise License, Premium License, Research License, Student License, Evaluation License,
+Decompression License or Distribution License) granted according to section 2; and/or b. non
+-compliant with any of sections 3a, 3c, 3e; and/or c. use of Genozip for which you were granted an
+Research or Student License to compress Your Commercial Data - shall be considered Severely
+Unauthorized Use of Genozip. In this case, You agree to a. pay Licensor US$100.00 for each file You
+compressed with Genozip b. that Licensor shall be eligible for 20% ownership of any revenue
+generated and intellectual property created that involved the Severely Unauthorized Use of Genozip.
+c. reimburse licensor for all legal and/or collection costs related to Your Severely Unauthorized
+Use of Genozip.
 
 5. Data collected. You consent to the following data collection:
 
@@ -120,9 +129,9 @@ hardware, operating system and IP address as displayed at end of the registratio
 
    b. When a file is compressed: a log record containing aggregate statistical information about
 the performance of the compression algorithm and associated metadata. This logging occurs when
-using a free license. When using a Paid Academic, Standard, Enterprise or Premium (i.e. paid)
-License, YOU WILL BE ASKED TO CHOOSE WHETHER OR NOT YOU ALLOW THIS LOGGING. Details can be found
-here: https://genozip.com/logs. 
+using a free license. When using a Research, Standard, Enterprise or Premium (i.e. paid) License,
+YOU WILL BE ASKED TO CHOOSE WHETHER OR NOT YOU ALLOW THIS LOGGING. Details can be found here: https
+://genozip.com/logs. 
 
 6. Mailing list. You consent to receiving low-frequency product announcement and other marketing
 emails related to Genozip.
@@ -164,5 +173,5 @@ ABOVE STATED REMEDY FAILS OF ITS ESSENTIAL PURPOSE.
 
 END OF TERMS AND CONDITIONS
 
-Genozip license version: 15.0.68
+Genozip license version: 15.0.69
 

RELEASE_NOTES.txt

@@ -3,6 +3,14 @@ Note on versioning:
 - Minor version changes with bug fixes and minor feature updates
 - Some minor versions are skipped due to failed deployment pipelines
 
+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 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. 

genozip.code-workspace

@@ -25,49 +25,20 @@
 		},
 		"files.associations": {
 			"*.vcf": "plaintext",
+			"*.sam": "plaintext",
+			"*.fq": "plaintext",
+			"*.fastq": "plaintext",
+			"*.fa": "plaintext",
+			"*.fna": "plaintext",
+			"*.fasta": "plaintext",
 			"*.eb": "python",
-			"genozip.h": "c",
-			"strings.h": "c",
-			"type_traits": "c",
-			"typeinfo": "c",
-			"piz.h": "c",
-			"sam_private.h": "c",
-			"errno.h": "c",
-			"*.data": "c",
-			"buffer.h": "c",
-			"profiler.h": "c",
-			"stats.h": "c",
-			"file.h": "c",
-			"*.tcc": "c",
-			"optional": "c",
-			"system_error": "c",
-			"array": "c",
-			"functional": "c",
-			"tuple": "c",
-			"utility": "c",
-			"endianness.h": "c",
-			"version.h": "c",
-			"libgen.h": "c",
-			"license.h": "c",
-			"windows.h": "c",
-			"cstdlib": "c",
-			"reconstruct.h": "c",
-			"seg.h": "c",
-			"compare": "c",
-			"context.h": "c",
-			"cmath": "c",
-			"zip.h": "c",
-			"limits": "c",
-			"algorithm": "c",
-			"atomic": "c",
-			"cstdint": "c",
-			"ratio": "c",
-			"random": "c",
-			"string": "c",
-			"string_view": "c",
-			"bzlib.h": "c",
-			"memory": "c",
-			"vector": "c"
-		}
+			"*.c": "c",
+			"*.h": "c",
+			"*.cpp": "cpp",
+			"*.bat": "bat",
+			"*.yaml": "yaml",
+			"*.sh": "shellscript",
+		},
+		"makefile.configureOnOpen": false
 	}
 }