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96 changes: 96 additions & 0 deletions CHANGELOG.md
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# Changelog

## [6.5.3](https://github.com/declanyewlim/GenomeKit/compare/v7.2.3...v6.5.3) (2026-03-03)


### ⚠ BREAKING CHANGES

* **appris/mane:** this change also fixes gencode.v41 to use the correct source (e107 now instead of e103).
* **vcfbin:** VCFTable.GT_HETEROZYGOUS is replaced with VCFTable.GT_HETEROZYGOUS_UNPHASED

### Features

* add appris data ([#132](https://github.com/declanyewlim/GenomeKit/issues/132)) ([6914b05](https://github.com/declanyewlim/GenomeKit/commit/6914b055d348892070be40c153f9d3e77adbc530))
* add gencode.v46 ([#181](https://github.com/declanyewlim/GenomeKit/issues/181)) ([8fdbc33](https://github.com/declanyewlim/GenomeKit/commit/8fdbc33a6be2f6d653cce596934919529eac0797))
* add gencode.v47 adjacent annos + appris ([#143](https://github.com/declanyewlim/GenomeKit/issues/143)) ([34b94df](https://github.com/declanyewlim/GenomeKit/commit/34b94dfd023dd56890b7d6a9bbad54738dec0876)), closes [#134](https://github.com/declanyewlim/GenomeKit/issues/134)
* add mouse annos and appris ([#137](https://github.com/declanyewlim/GenomeKit/issues/137)) ([3e2b148](https://github.com/declanyewlim/GenomeKit/commit/3e2b14844a3ec818f8f4fe6f1084e95483810662)), closes [#129](https://github.com/declanyewlim/GenomeKit/issues/129)
* compatibility with python 3.10 ([#28](https://github.com/declanyewlim/GenomeKit/issues/28)) ([1d51397](https://github.com/declanyewlim/GenomeKit/commit/1d51397db0f84cb5d543f6dc9de331871ff1c6ab))
* deprecate py38, support py11 py12 ([#101](https://github.com/declanyewlim/GenomeKit/issues/101)) ([cd94123](https://github.com/declanyewlim/GenomeKit/commit/cd941236dd57abbb9f477e8fec89513c88775617))
* **gtrack:** inplace output ([#73](https://github.com/declanyewlim/GenomeKit/issues/73)) ([17838b7](https://github.com/declanyewlim/GenomeKit/commit/17838b7a7b78aa067eecf817193bee1ec07f9245))
* **gtrack:** interval iteration ([#71](https://github.com/declanyewlim/GenomeKit/issues/71)) ([1e2b672](https://github.com/declanyewlim/GenomeKit/commit/1e2b67222fd3504dfd112925893f633bf665f11c))
* list available genome configs ([#549](https://github.com/declanyewlim/GenomeKit/issues/549)) ([#19](https://github.com/declanyewlim/GenomeKit/issues/19)) ([fb9776c](https://github.com/declanyewlim/GenomeKit/commit/fb9776cd78b296cdb7cdd903d052a0ed6c68178a))
* modernize usage of setuptools ([#176](https://github.com/declanyewlim/GenomeKit/issues/176)) ([412a00d](https://github.com/declanyewlim/GenomeKit/commit/412a00da0ab3b77df72cc729441e57b30edf4f95))
* publish pip wheels for linux+mac ([#163](https://github.com/declanyewlim/GenomeKit/issues/163)) ([100cc81](https://github.com/declanyewlim/GenomeKit/commit/100cc8141477769027ab981a6d5861b51ebc5e6a))
* read/write files for refg name hash lookups ([#62](https://github.com/declanyewlim/GenomeKit/issues/62)) ([8074701](https://github.com/declanyewlim/GenomeKit/commit/80747011a83d731b7e1f594e98f1996ac69085fd))
* S3 data manager ([#121](https://github.com/declanyewlim/GenomeKit/issues/121)) ([85f1cbd](https://github.com/declanyewlim/GenomeKit/commit/85f1cbd93f17235e195a026e19db6509d43c44a2))
* support gencode v47 ([#131](https://github.com/declanyewlim/GenomeKit/issues/131)) ([210ec32](https://github.com/declanyewlim/GenomeKit/commit/210ec329e487949b431f0262bdad9de1ecbcbf22))
* support gencode vM31 appris ([#197](https://github.com/declanyewlim/GenomeKit/issues/197)) ([f0c6222](https://github.com/declanyewlim/GenomeKit/commit/f0c6222d0343f7e20c0bb788667cc94dc7482333))
* support MANE Select and Clinical Plus transcripts ([#127](https://github.com/declanyewlim/GenomeKit/issues/127)) ([98d0757](https://github.com/declanyewlim/GenomeKit/commit/98d075746d3c8a8937149e498d8fef85e1579db1))
* support refseq anno GCF_000001405.40-RS_2024_08 ([#125](https://github.com/declanyewlim/GenomeKit/issues/125)) ([b8e1ca3](https://github.com/declanyewlim/GenomeKit/commit/b8e1ca35116b4d6b4ac04f5d3526f12786a02b05)), closes [#124](https://github.com/declanyewlim/GenomeKit/issues/124)
* use new dedicated requester-pays public bucket ([#33](https://github.com/declanyewlim/GenomeKit/issues/33)) ([e4fb7a1](https://github.com/declanyewlim/GenomeKit/commit/e4fb7a196e0201d653e7a563ca2150c393a0e749))
* **vcfbin:** support phased VCF ([#92](https://github.com/declanyewlim/GenomeKit/issues/92)) ([a1f0b2a](https://github.com/declanyewlim/GenomeKit/commit/a1f0b2ad8a86b21dcf68134e9e8c87ce9f79d665))
* wheel distribution for linux on python 3.9-3.12 ([#150](https://github.com/declanyewlim/GenomeKit/issues/150)) ([6faecce](https://github.com/declanyewlim/GenomeKit/commit/6faecce77546c3ed0c0433b5a8f2e134463b1c86))
* wheel distribution for linux on python 3.9-3.12, arm architecture ([#156](https://github.com/declanyewlim/GenomeKit/issues/156)) ([4a3ed58](https://github.com/declanyewlim/GenomeKit/commit/4a3ed587768c77a5ee7482359d512320b0c8ea6f))


### Bug Fixes

* add condition for prepending chr to variant chromosome ([#195](https://github.com/declanyewlim/GenomeKit/issues/195)) ([8abe006](https://github.com/declanyewlim/GenomeKit/commit/8abe0065b5ad77372f2cad9f7b21c7025a41f183))
* allow local-only files to be loaded ([#38](https://github.com/declanyewlim/GenomeKit/issues/38)) ([a56a5dc](https://github.com/declanyewlim/GenomeKit/commit/a56a5dc690d507a04b429956b5b3fb96e64839d8)), closes [#37](https://github.com/declanyewlim/GenomeKit/issues/37)
* allow VariantGenome to be serialized ([#161](https://github.com/declanyewlim/GenomeKit/issues/161)) ([18f3253](https://github.com/declanyewlim/GenomeKit/commit/18f32537acaced5a410e937de5bc48f5ae3088f7))
* **appris/mane:** allow data source to determine availability ([#157](https://github.com/declanyewlim/GenomeKit/issues/157)) ([41c1fbe](https://github.com/declanyewlim/GenomeKit/commit/41c1fbe5c011d04504b08eef4435c50771c01471))
* assert that appris transcripts match the requested gene ([#70](https://github.com/declanyewlim/GenomeKit/issues/70)) ([fd93609](https://github.com/declanyewlim/GenomeKit/commit/fd93609f13d67d3eac84aae3591d30a833108c4f))
* avoid accessing released memory ([#63](https://github.com/declanyewlim/GenomeKit/issues/63)) ([1ab7456](https://github.com/declanyewlim/GenomeKit/commit/1ab74561c5a80ed5a4c47c02c8cbdeb55040260c))
* avoid errors when blob metadata is None ([#54](https://github.com/declanyewlim/GenomeKit/issues/54)) ([e850c54](https://github.com/declanyewlim/GenomeKit/commit/e850c5417f285e2f4f82d30cff2555c12e590be9))
* avoid user confusion when loading annotation ([#53](https://github.com/declanyewlim/GenomeKit/issues/53)) ([e556030](https://github.com/declanyewlim/GenomeKit/commit/e556030bebd2c214ada791909925fa151a016017))
* broken installation on osx-arm64 ([#65](https://github.com/declanyewlim/GenomeKit/issues/65)) ([6bd68c2](https://github.com/declanyewlim/GenomeKit/commit/6bd68c2ae79ac37cca1b01a9dc3cde582c92bfa2))
* build all supported MANE annotations ([#185](https://github.com/declanyewlim/GenomeKit/issues/185)) ([e369690](https://github.com/declanyewlim/GenomeKit/commit/e3696907f5f6d8c9c9c842d19b92059c79b55909))
* build anno relies on utr/cds ordering ([#142](https://github.com/declanyewlim/GenomeKit/issues/142)) ([e28678b](https://github.com/declanyewlim/GenomeKit/commit/e28678b3778baa8fff6a54ab4858eb794f8b53c2)), closes [#135](https://github.com/declanyewlim/GenomeKit/issues/135)
* check genome.dna(Interval) arg type ([#68](https://github.com/declanyewlim/GenomeKit/issues/68)) ([f7b6e5c](https://github.com/declanyewlim/GenomeKit/commit/f7b6e5c998b8492cb5142b4fb83a5c3b86c4c49f)), closes [#67](https://github.com/declanyewlim/GenomeKit/issues/67)
* **data:** exception raising was dependent on an envvar before ([#99](https://github.com/declanyewlim/GenomeKit/issues/99)) ([3d461c1](https://github.com/declanyewlim/GenomeKit/commit/3d461c184d71eaca48bebc60f1f40dcba95fcafe))
* **dna:** consistent allow_outside_chromosome defaults ([#98](https://github.com/declanyewlim/GenomeKit/issues/98)) ([611970d](https://github.com/declanyewlim/GenomeKit/commit/611970d9b1c6cfaca2e2dd7938ec9d3d46cef697))
* ensure correctness of signed/unsigned comparisons ([#55](https://github.com/declanyewlim/GenomeKit/issues/55)) ([23c1d03](https://github.com/declanyewlim/GenomeKit/commit/23c1d0356a582933c8971f3eef408562727c18a6))
* handle anchor within deletions ([#140](https://github.com/declanyewlim/GenomeKit/issues/140)) ([3c8aabb](https://github.com/declanyewlim/GenomeKit/commit/3c8aabbd7bbc29f4771560cb4b47c65f27056c9d))
* intersect() with mismtached chrom ([#191](https://github.com/declanyewlim/GenomeKit/issues/191)) ([8c59110](https://github.com/declanyewlim/GenomeKit/commit/8c59110c5be29a00dad0837e0fcb0598262b97be)), closes [#189](https://github.com/declanyewlim/GenomeKit/issues/189)
* missing mock for dna boundary ([#25](https://github.com/declanyewlim/GenomeKit/issues/25)) ([b058b53](https://github.com/declanyewlim/GenomeKit/commit/b058b5380a98f0b7766f4fa9de880085d0935a1d))
* propagate errors when datamanager fails to resolve paths for a refg ([#172](https://github.com/declanyewlim/GenomeKit/issues/172)) ([00d61c7](https://github.com/declanyewlim/GenomeKit/commit/00d61c770779fd281f3731bf34b89411f99b83d3))
* provide a better hint in case of permissions error ([#42](https://github.com/declanyewlim/GenomeKit/issues/42)) ([cb21280](https://github.com/declanyewlim/GenomeKit/commit/cb212800dd9017b3627ce1d6093da9e0fa3c4d3f))
* **track:** check inplace dtype ([#79](https://github.com/declanyewlim/GenomeKit/issues/79)) ([5a2cb38](https://github.com/declanyewlim/GenomeKit/commit/5a2cb3895565846ae0440d59da120ee7ca8bc6e0))
* **track:** handle res>1 for track interval interrogation ([#84](https://github.com/declanyewlim/GenomeKit/issues/84)) ([246a6dc](https://github.com/declanyewlim/GenomeKit/commit/246a6dc26f524aa70cb9c21c0c5ab9c2d0caeff5))
* **track:** OOB issue with negative strands on u1 tracks ([#104](https://github.com/declanyewlim/GenomeKit/issues/104)) ([53ae2f5](https://github.com/declanyewlim/GenomeKit/commit/53ae2f5881c2c97b572cb787098544f59e2e2d14))
* **track:** segfault when decoding large dims ([#75](https://github.com/declanyewlim/GenomeKit/issues/75)) ([6f5c29e](https://github.com/declanyewlim/GenomeKit/commit/6f5c29ec610018994f0d451624edad0053013c15))
* **track:** sparse encoding broken ([#88](https://github.com/declanyewlim/GenomeKit/issues/88)) ([c8f6732](https://github.com/declanyewlim/GenomeKit/commit/c8f6732e1be4325e56675c958c852a24a652056b))
* **track:** strided decoding ([#77](https://github.com/declanyewlim/GenomeKit/issues/77)) ([1fc1b37](https://github.com/declanyewlim/GenomeKit/commit/1fc1b378875a0376c7f7d41a1335a8cccc1b8325))


### Documentation

* acknowledge past contributors ([#43](https://github.com/declanyewlim/GenomeKit/issues/43)) ([d0dcfd5](https://github.com/declanyewlim/GenomeKit/commit/d0dcfd5df09b1f36e0627031bad6461766b24b12))
* clarify how to get a list of all genomes ([#182](https://github.com/declanyewlim/GenomeKit/issues/182)) ([912b201](https://github.com/declanyewlim/GenomeKit/commit/912b201c3cd7310984bd554a4050cab4e4d6b088))
* more standard cmake instructions ([#21](https://github.com/declanyewlim/GenomeKit/issues/21)) ([55a73d8](https://github.com/declanyewlim/GenomeKit/commit/55a73d86301b9514f1e5df5c98428e4f1eb3d464))
* prepare required documentation for AWS Open Data ([#116](https://github.com/declanyewlim/GenomeKit/issues/116)) ([364d723](https://github.com/declanyewlim/GenomeKit/commit/364d72323eaee22147064f7ad6d7027dbafea384))
* provide a data starter script ([#39](https://github.com/declanyewlim/GenomeKit/issues/39)) ([a257da1](https://github.com/declanyewlim/GenomeKit/commit/a257da1954e750209a0df9848b5d998901dc3d7f))
* restore and document link to versionized docs ([#51](https://github.com/declanyewlim/GenomeKit/issues/51)) ([cc22955](https://github.com/declanyewlim/GenomeKit/commit/cc22955ec125d7f802ff1a2d42eec20dc16f8db8)), closes [#50](https://github.com/declanyewlim/GenomeKit/issues/50)
* show project description on https://pypi.org/project/genomekit/ ([#164](https://github.com/declanyewlim/GenomeKit/issues/164)) ([f13ed06](https://github.com/declanyewlim/GenomeKit/commit/f13ed06d90d2ddc0856b4749f323de2d7852ede8))
* simplify strandedness instructions for bedgraph/wig ([#118](https://github.com/declanyewlim/GenomeKit/issues/118)) ([60c44dd](https://github.com/declanyewlim/GenomeKit/commit/60c44ddedd09fdd713ace12e18d5fa34ce844e15))
* starter_build script download ([#96](https://github.com/declanyewlim/GenomeKit/issues/96)) ([1245558](https://github.com/declanyewlim/GenomeKit/commit/12455581374025313e767a6fdfef96b23a77987e))


### Miscellaneous Chores

* avoid CI failure on conda-forge ([#3](https://github.com/declanyewlim/GenomeKit/issues/3)) ([468272e](https://github.com/declanyewlim/GenomeKit/commit/468272eb8a0debaaa245771ba64b8017b8dfd247))
* avoid compile error on mac ([#5](https://github.com/declanyewlim/GenomeKit/issues/5)) ([1f9d59e](https://github.com/declanyewlim/GenomeKit/commit/1f9d59e35bc66e6c6ae87f7cc12aa6db06dc72a6))
* avoid import on Windows ([#15](https://github.com/declanyewlim/GenomeKit/issues/15)) ([0aef946](https://github.com/declanyewlim/GenomeKit/commit/0aef9466fbcea725f16f731e8ce7e499b78d0e32))
* avoid some tests on windows ([#7](https://github.com/declanyewlim/GenomeKit/issues/7)) ([7359a45](https://github.com/declanyewlim/GenomeKit/commit/7359a450de76cefba51a14dc74c42f659e230ce5))
* fix windows build ([#106](https://github.com/declanyewlim/GenomeKit/issues/106)) ([e1754c7](https://github.com/declanyewlim/GenomeKit/commit/e1754c71a7b1787e12a3c88ef98a65e1106b0094))
* move releases to conda-forge ([#1](https://github.com/declanyewlim/GenomeKit/issues/1)) ([c2ddf93](https://github.com/declanyewlim/GenomeKit/commit/c2ddf932ec83acd3483d472dda6eddbdf3b4d4ea))
* reenable tests on windows ([#13](https://github.com/declanyewlim/GenomeKit/issues/13)) ([fb90358](https://github.com/declanyewlim/GenomeKit/commit/fb9035829806da8ebc2fbfbd627e75c1803f4472))
* release 5.0.0 ([#36](https://github.com/declanyewlim/GenomeKit/issues/36)) ([cc939ef](https://github.com/declanyewlim/GenomeKit/commit/cc939ef03a039703a0138d60d8ce1ed5709c8a26))
* release 6.0.3 ([e3ff39e](https://github.com/declanyewlim/GenomeKit/commit/e3ff39e2ed0988858a05ceabdc9186d8dc9f73b8))
* release 6.0.3 ([#110](https://github.com/declanyewlim/GenomeKit/issues/110)) ([f8a1062](https://github.com/declanyewlim/GenomeKit/commit/f8a10626f84bc93082e66ad00b822a2106b44046))
* release 6.1.1 ([#119](https://github.com/declanyewlim/GenomeKit/issues/119)) ([e081b55](https://github.com/declanyewlim/GenomeKit/commit/e081b55cf3cd29b306510d69dc5db7a2fc0cbb67))
* release 6.5.3 ([#152](https://github.com/declanyewlim/GenomeKit/issues/152)) ([49633a8](https://github.com/declanyewlim/GenomeKit/commit/49633a81fd6f6b606d7b19d79aa909ae2bed5c64))
* replace libfmt with std::format ([#148](https://github.com/declanyewlim/GenomeKit/issues/148)) ([ae7100a](https://github.com/declanyewlim/GenomeKit/commit/ae7100ab1462aa07cdce03a3975a04a4e561cd7d))
* revert the windows test change ([#11](https://github.com/declanyewlim/GenomeKit/issues/11)) ([879adb5](https://github.com/declanyewlim/GenomeKit/commit/879adb54963ba7788d681108ca8f494f27637790))
* skip bioconda-dependant tests on conda-forge ([#17](https://github.com/declanyewlim/GenomeKit/issues/17)) ([cad0584](https://github.com/declanyewlim/GenomeKit/commit/cad0584f84cf494a1bf6a17efdbabda1c26ec8f0))
* skip gcs-dependent tests on conda-forge ([#23](https://github.com/declanyewlim/GenomeKit/issues/23)) ([1595cba](https://github.com/declanyewlim/GenomeKit/commit/1595cba8c0071b6ae127aff482cbc9ca5c96ff92))
* skip windows tests correctly ([#9](https://github.com/declanyewlim/GenomeKit/issues/9)) ([ce7f1b3](https://github.com/declanyewlim/GenomeKit/commit/ce7f1b3d728e71acf910930c3e900b6899966bf0))

## [7.2.3](https://github.com/deepgenomics/GenomeKit/compare/v7.2.2...v7.2.3) (2026-01-30)


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2 changes: 1 addition & 1 deletion setup.py
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"twobitreader>=3.1",
]

version = "7.2.3"
version = "6.5.3"

# See https://stackoverflow.com/questions/9977889/how-to-include-license-file-in-setup-py-script/66443941#66443941
class egg_info_ex(egg_info):
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