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charite / jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)
http://jannovar.readthedocs.io/en/master/
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Bump com.github.samtools:htsjdk from 2.20.3 to 4.0.2 #588

Closed dependabot[bot] closed 1 year ago

dependabot[bot] commented 1 year ago

Bumps com.github.samtools:htsjdk from 2.20.3 to 4.0.2.

Release notes

Sourced from com.github.samtools:htsjdk's releases.

4.0.2

Small release with a few bug fixes and small features.

What's Changed

New Contributors

Full Changelog: https://github.com/samtools/htsjdk/compare/4.0.1...4.0.2

4.0.1

This is a tiny release which bumps some dependency versions and adds two small convenience methods to Genotype.

What's Changed

Full Changelog: https://github.com/samtools/htsjdk/compare/4.0.0...4.0.1

4.0.0

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 updated dependencies to fix security issues. There are several small bug fixes as well.

JSON dependency:

We've dropped the MJSON library which was no longer being updated and replaced it with a similarly small json library from org.json

What's Changed

New Contributors

Full Changelog: https://github.com/samtools/htsjdk/compare/3.0.5...4.0.0

3.0.5

... (truncated)

Commits
  • 3964abe Update test dependencies to newest versions (#1690)
  • 5f0d484 Fix IOUtil.unrollPaths for http paths with query parameters (#1688)
  • 6d1a796 Update some methods in BamFileIoUtils accept Path input (#1681)
  • c6b1fe1 Support lenient (optimistic) read-only VCF 4.4. (#1683)
  • 85a0f0f Update snappy-java (#1687)
  • 38dbd0e Add IntervalFileFeature for common interface to name in bed or interval_list ...
  • 5cc90ed Update two remaining out of date dependencies (#1677)
  • 1e5ec5a Add new Genotype methods hasRefAllele and hasAltAllele (#1678)
  • 20334af Move the EnaRefServiceTest to the externalAPI test group (#1675)
  • 75eac46 add SINGULAR platform to read group (#1635)
  • Additional commits viewable in compare view


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