TileDB-VCF 0.40.1

What's Changed

• Bump nightly build release branch to 2.30 by @jdblischak in #864
• Reduce memory consumption when a single position returns many samples by @alancleary in #867
• Remove deprecated progress estimation by @alancleary in #868
• Update region_partition and sample_partition parameter descriptions by @alancleary in #869
• Pinned pandas version to avoid installation of version 3.0.0 by @alancleary in #870
• Fix read_variant_stats() segfault when region is empty by @alancleary in #871

Full Changelog: 0.40.0...0.40.1

TileDB-VCF 0.40.0

What's Changed

Breaking change: The vcf_headers array is now registered under the metadata group rather than the top level VCF group.

• Update TileDB core to 2.30.0 by @jp-dark in #860
• Add support for Carrara URIs by @XanthosXanthopoulos in #862

TileDB-VCF 0.40.0rc0

What's Changed

Breaking change: The vcf_headers array is now registered under the metadata group rather than the top level VCF group.

• Update TileDB core to 2.30.0 by @jp-dark in #860
• Add support for Carrara URIs by @XanthosXanthopoulos in #862

TileDB-VCF 0.39.2

What's Changed

• Add a new Assets directory to examples by @nickvigilante in #849

• Add pre-commit by @alancleary in #853

• Consolidate URI functions by @alancleary in #851

• Improve API for VCF read_variant_stats() and read_allele_count() by @alancleary in #852

• Update TileDB core to 2.29.2 by @alancleary in #858

Full Changelog: 0.39.1...0.39.2

TileDB-VCF 0.39.1

What's Changed

• [Backport release-0.39] Update TileDB core to 2.29.1 by @github-actions[bot] in #848

Full Changelog: 0.39.0...0.39.1

TileDB-VCF 0.39.0

What's Changed

• Updated HTSlib to version 1.22.1 by @alancleary in #822
• Improve run-time performance of delete exporter by @alancleary in #833
• Update the Buffer class data() method to compute string view directly from offsets by @alancleary in #834
• Deletion memory usage by @alancleary in #835
• Update Docker commands since ENTRYPOINT was removed by @jdblischak in #838
• Disable dangling reference errors when compiling with GCC 14 by @alancleary in #837
• Add arm64 linux source download by @sounkou-bioinfo in #839
• Update TileDB core to 2.29.0 by @github-actions[bot] in #846

New Contributors

• @sounkou-bioinfo made their first contribution in #839

Full Changelog: 0.38.0...0.39.0

TileDB-VCF 0.38.2

What's Changed

• Improve run-time performance of sample deletion by @alancleary in #833 and #834
• Constrain and parameterize sample deletion memory usage by @alancleary in #835

Full Changelog: 0.38.1...0.38.2

TileDB-VCF 0.38.1

What's Changed

• Bump nightly build release branch to 2.28 by @jdblischak in #819
• Fix img and academy links by @leipzig in #815
• Remove ENTRYPOINT for Nextflow compatibility by @leipzig in #816
• Updated HTSlib to version 1.22.1 by @alancleary in #822
• Update TileDB Embedded to 2.28.1 by @alancleary in #826

Full Changelog: 0.38.0...0.38.1

TileDB-VCF 0.38.0

What's Changed

• Update TileDB to release 2.28.0 (PR #818)
• Retry vcf_open up to 3 times (PR #801)

Full Changelog: 0.37.0...0.38.0

0.37.0

What's Changed

• Remove Spark and Dask support by @gspowley in #786
• Change VLA code by using std::vector by @dudoslav in #787
• Migrate to macos-13 runner image by @dudoslav in #793
• Run CI on Ubuntu 24 (GCC 13) by @jdblischak in #788
• More robust non-empty buffer check during ingestion by @gspowley in #792
• Upgrade to TileDB 2.27.0 by @gspowley in #789
• Remove spark asset release CI stage by @gspowley in #794

Deprecations

• Spark and Dask are no longer supported.

New Contributors

• @dudoslav made their first contribution in #787

Full Changelog: 0.36.0...0.37.0