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htsjdk 5.0.0 https://github.com/samtools/htsjdk/releases/tag/5.0.0

Release 5.0.0 · samtools/htsjdk

htsjdk 5.0.0 Release Notes This is a major release. The headline work is CRAM 3.1 write support (closing the loop on the codec work in 4.2.0 and the read-side wiring in 4.3.0), a set of substantial...

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Pierre Lindenbaum Mar 30

RE: https://genomic.social/@yokofakun/115740891523944578

https://github.com/samtools/htsjdk/discussions/1760#discussioncomment-16384234

> HTSJDK has not been the most actively maintained project for a long time, and with many departures from Broad in the last couple of years, it's not clear to me who still has an active interest in helping maintain the project.

#java #htsjdk #samtools

Pierre Lindenbaum Dec 18

PR for #htsjdk : https://github.com/samtools/htsjdk/pull/1751 "optimistic_vcf_4_x "

support for VCF4.5 just like (vcf4.4) . Changed optimistic_vcf_4_4 to optimistic_vcf_4_x by lindenb · Pull Request #1751 · samtools/htsjdk

Description This PR add a support to vcf4.5 just like vcf4.4. I changed things like optimistic_vcf_4_4 to optimistic_vcf_4_x. The PR adds a new VCFHeaderVersion 4_5 The PR adds a new VCF header 4.5...

GitHub

Pierre Lindenbaum Oct 29, 2024

htsjdk pull request accepted https://github.com/samtools/htsjdk/pull/1726 🥳 #htsjdk #java #bioinformatics

improve gff: add Locatable to Gff3BaseData, add 'Optional<String> getAttr(key)' and 'hasAttribute' by lindenb · Pull Request #1726 · samtools/htsjdk

Description This PR improves the GFF3 classes: 99% the interesting attributes in a GFF3 file are unique (for example gene_biotype, gene_name, etc...) , so using the function List<String> ge...

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Pierre Lindenbaum Aug 4, 2023

Java API for high-throughput #sequencing data (#HTS) formats. version 4.0.0 released. "This is the first release to be built exclusively for #java 17." #htsjdk https://github.com/samtools/htsjdk/releases/tag/4.0.0

Release 4.0.0 · samtools/htsjdk

Moving forward This is the first release to be built exclusively for java 17. Java 17 features are now allowed in our source code and we will no longer support older versions of java. We've also ...

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Pierre Lindenbaum Mar 16, 2023

I submitted a first PR for #htsjdk to support the #gtf format : https://github.com/samtools/htsjdk/pull/1662

#java #htsjdk #bioinformatics #git

proposal for a package htsjdk.tribble.gtf by lindenb · Pull Request #1662 · samtools/htsjdk

Hi all, here is a proposal for a new package htsjdk.tribble.gtf Description htsjdk contains a gff3 codec but is still missing a GTF codec. I wrote a few classes parsing the a GTF. Some parts were c...

GitHub

Pierre Lindenbaum Feb 22, 2023

#htsjdk 3.0.5 released https://github.com/samtools/htsjdk/releases/tag/3.0.5

Release 3.0.5 · samtools/htsjdk

The last gasp of Java 8 This release includes very minor new features as well as a bug fix. It is mostly notable because it is intended to be the last release supporting Java 8. Future releases w...

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Pierre Lindenbaum Feb 22, 2023

future releases of #htsjdk will target #Java 17 https://github.com/samtools/htsjdk/discussions/1656

3.0.5 · Discussion #1656 · samtools/htsjdk

The last gasp of Java 8 This release includes very minor new features as well as a bgu fix. It is mostly notable because it is intended to be the last release supporting Java 8. Future releases wil...

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Markus Eisele Dec 3, 2022

#HTSJDK is an implementation of a unified #Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. https://bit.ly/3U2qksu