{"bugs":[{"bugid":741540,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"UNCONFIRMED","summary":"sci-biology\/bcftools-1.10.2 - support for extra features is disabled without a USE flag"}],"categories":[{"categoryid":450,"name":"dev-lang","summary":"The dev-lang category contains various programming language implementations and related tools."},{"categoryid":336,"name":"dev-python","summary":"The dev-python category contains packages whose primary purpose is to provide Python modules, extensions and bindings, as well as tools and utilities useful for development in the Python programming language."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":318,"name":"sci-libs","summary":"The sci-libs category contains various science-related libraries."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"475132eba5890f664da63578d19d64bccecc63af","committime":"2026-02-02T16:15:50","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"62cbc4def11dc8e47d228cc573ace4698370e073","committime":"2026-02-02T16:03:49","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.23"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"0d4b297c345fb6a401e341d0e1b69f4877bdaa2a","committime":"2025-11-29T13:45:45","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"abdd260168c6e08cf711889889e7b258a85b3a56","committime":"2025-11-29T13:40:20","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: bring back 1.21 for pysam"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"0665ef749aca9e946a85ab6198236f201ee99ceb","committime":"2025-11-29T13:30:45","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"980fdc05a826fa593619e537bc7936453e3130d9","committime":"2025-11-29T13:17:10","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: drop 1.19, 1.21"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"00b4cc6bb3b864fbeaa6dca1da399c3716afed16","committime":"2025-11-04T09:50:46","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Done via:\n\n```\ngit grep -l virtual\/zlib$ | xargs sed -i -e 's@virtual\/zlib$@&:=@'\n```\n\nSigned-off-by: Michał Górny <mgorny@gentoo.org>","commitid":"6a3644bf2f9aace46ad9bbab2e4f3bccd747079e","committime":"2025-11-04T09:36:27","packageid":67995,"repoid":1,"summary":"*\/*: Add := to virtual\/zlib deps, part 1"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"5a1adb610b1d91ab6683cbe671e266f424224c16","committime":"2025-11-04T08:35:48","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Update done using:\n\n```\ngit grep -l sys-libs\/zlib dev-* | xargs sed -i -e s@sys-libs\/zlib@virtual\/zlib@g\ngit diff --name-only | xargs copybump\ngit diff --name-only | xargs grep -l PYTHON_COMPAT | xargs gpy-impl -@dead\npkgcheck scan --commits -c SourcingCheck,VisibilityCheck --exit error\n```\n\nSigned-off-by: Michał Górny <mgorny@gentoo.org>","commitid":"f1351833569f8b22abc3dc9e74abeed7e8641096","committime":"2025-11-04T08:17:06","packageid":67995,"repoid":1,"summary":"sci-*\/*: update for virtual\/zlib"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"5636995d406685527919d45bbe44c1f8a8c1fcdd","committime":"2025-06-22T15:52:13","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"a05f47085384c3ab44d448976fca34cd287554dc","committime":"2025-06-22T15:33:13","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.22"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"45a8c91b24abd9c783b90a37eb4acca7613a0c93","committime":"2025-03-21T15:05:11","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"quincyf467@protonmail.com","authorname":"Quincy Fleming","body":"Signed-off-by: Quincy Fleming <quincyf467@protonmail.com>\nSigned-off-by: Nowa Ammerlaan <nowa@gentoo.org>","commitid":"76e614ae05dbb35ecbbf3a7728d46b8e7701a0af","committime":"2025-03-14T23:27:58","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.21"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"02e5e751049cd4311fd9db8c4d4647800e60b609","committime":"2024-05-24T09:03:45","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"4cb73988356dd75b6f43951f9e84858bac7f947f","committime":"2024-05-24T08:59:51","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.20"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"1af696627e09436ead88952c730660ff081c60ba","committime":"2024-05-24T08:59:45","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: drop 1.17"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"c712b4a4f5e2d22b9b99cd7be1333e5bf279ce88","committime":"2024-03-26T11:18:41","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"9e53125a7a6ae8c74dc0b154c9f14498a4bbfb0d","committime":"2024-03-26T11:06:22","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.19"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"735d7f5411f2dac24191880c654556cc7e42271e","committime":"2023-04-06T19:31:44","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"a70b50ddac48495aa2104769f34d19c007cf1861","committime":"2023-04-06T19:29:08","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: drop 1.16"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"131761f618321780511172e7b352f842d5c0b70e","committime":"2023-03-30T11:16:45","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"44c2c0b7d6006ee664863ccaf60bbde18a7a2153","committime":"2023-03-30T11:11:00","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.17"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"89d8cba905e693594e0095b73d036c7f1d26527a","committime":"2023-02-19T15:46:53","packageid":67995,"repoid":1,"summary":"Merge updates from 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CI","commitid":"6e318a7ce0c6eb0732e59de3f8932a8ac7022910","committime":"2022-12-27T00:18:04","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"01090e63f3067303d6ca41e5bbea8b890bbab7b6","committime":"2022-12-27T00:06:46","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.16"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e00f3bf79ece7f33a551fdf890b813179ead94d5","committime":"2022-06-19T08:18:46","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"7b77e6902ea23156a82fa792758968421aae9342","committime":"2022-06-19T08:08:44","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: drop 1.13, 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<soap@gentoo.org>","commitid":"65bf4360727a6bceed339106305247eb0962f654","committime":"2022-03-19T11:38:05","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.15"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4e0f7fb7e8024d50131b72ba4c2d56a152ce2d3d","committime":"2021-10-11T15:06:24","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"0c0f7543e2f922af5b5198b2abb6d9c32b6be5cb","committime":"2021-10-11T14:55:09","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: drop 1.10.2"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"376defb3c9166b6757ccf97bf7439cfb268fe7de","committime":"2021-10-03T17:51:09","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"9eab85fba2bfef0ad9b849a75a7e78d2895d4eba","committime":"2021-10-03T17:41:38","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: add 1.13"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"81ea93ee3abaa45450db8d93c33d45bd29ad4053","committime":"2021-07-17T18:36:25","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert <soap@gentoo.org>","commitid":"56596ea51bf5e695852b6cd01fe983b6f8ac7747","committime":"2021-07-17T18:16:57","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: PYTHON_MULTI_USEDEP -> PYTHON_USEDEP"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"2c6c2efe4c1a02689bcd5e6e58a54035dec44025","committime":"2021-01-31T02:18:05","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny <mgorny@gentoo.org>","commitid":"d8cbaa62dbf4abc31cc74d2cc12e3d0c7ac9b70a","committime":"2021-01-30T23:36:06","packageid":67995,"repoid":1,"summary":"*\/*: Remove obsolete values from PYTHON_COMPAT"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"3ddff3fd2ce17b27658777001c77412490fdbddf","committime":"2020-08-03T21:35:14","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.1, Repoman-2.3.23\nSigned-off-by: David Seifert <soap@gentoo.org>","commitid":"5fa92ad679d028ae8e8b88fc044bbbacd475780d","committime":"2020-08-03T21:11:15","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: Remove old"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"b503e6b8ce1cfc6365abe5c16cfb25872a1aad9d","committime":"2020-08-03T17:05:18","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.1, Repoman-2.3.23\nSigned-off-by: David Seifert <soap@gentoo.org>","commitid":"fbdda699ffc5db18d5dc0b5e2c59cf511dec93b5","committime":"2020-08-03T16:54:26","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: Bump to version 1.10.2"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"a8564b8958715f71175a3b8de8f2a746f033e84f","committime":"2020-03-27T11:07:37","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.96, Repoman-2.3.22\nSigned-off-by: David Seifert <soap@gentoo.org>","commitid":"d63ea201e68952da8f5083002aedb951e4c11551","committime":"2020-03-27T10:35:21","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: Add python 3.7"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"07af4f23e380253ca997a7779660947173e0aa07","committime":"2020-02-09T17:30:17","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny <mgorny@gentoo.org>","commitid":"4394f8b4a2879971798e2bb96736b3c4dec092f0","committime":"2020-02-07T17:56:15","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: Switch to PYTHON_MULTI_USEDEP API"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"7e3818cf12463373388224f872925bcc112f6594","committime":"2020-02-07T10:06:28","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mmokrejs@gmail.com","authorname":"Martin Mokrejs","body":"From NEWS one can infer bcftools was at least from about 1.7 version\npython3 compatible. Moreover, at the moment the shenbang lines specifically\ncall python3.6. So, adjust the PYTHON_COMPAT accordingly. matplotlib is\nused by the python scripts, unconditionally.\n\nPackage-Manager: Portage-2.3.84, Repoman-2.3.20\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/14421\nSigned-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>\nSigned-off-by: David Seifert <soap@gentoo.org>","commitid":"d6e49da338f6a6ce88c7bab2a4bbb643d603d95b","committime":"2020-02-07T09:42:34","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: fix PYTHON_COMPAT, add missing matplotlib dep"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"fde58f2c9211641a64be317bec48bbe36a815062","committime":"2018-10-28T20:44:04","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/647714\nSigned-off-by: David Seifert <soap@gentoo.org>\nPackage-Manager: Portage-2.3.50, Repoman-2.3.11","commitid":"59ee040ec29f25e981534026d9be99b4ca36b458","committime":"2018-10-28T20:24:40","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: Version bump to 1.9"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"299bb59f5cb803e437aa028d8dd5b082e923ab4f","committime":"2017-09-02T12:45:26","packageid":67995,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.8, Repoman-2.3.3","commitid":"a26495e2ae69026f4ad9d7a730611a1cac92448e","committime":"2017-09-02T12:33:32","packageid":67995,"repoid":1,"summary":"sci-biology\/bcftools: Add 1.5 from sci overlay"}],"dependencies":[{"block":false,"categoryid":336,"description":"Pure python plotting library with matlab like syntax","ebuildids":[827635,827635,868034,868034,868034,883136,883136,883136,888652,888652,888652,888652],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"python@gentoo.org","maintainername":"Python","name":"matplotlib","packageid":41930,"summary":"matplotlib is an interactive library for plotting and doing basic data analysis in python with a syntax similar to matlab. 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