All File Changes

v468_preview to v468_preview2 (2024-07-01 to 2024-07-08) v468

• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 8, context: html, text, full: html, text
    b0d399498f44f25274a920db635078590582230e Tue Jul 2 15:18:44 2024 -0700
    Adding documentation and an example for getting the reverse complement sequence using the API, refs #26691
  • lines changed 38, context: html, text, full: html, text
    f8ec1e5046ba29f263a9483fe00ee7b9da0af206 Thu Jul 4 08:20:03 2024 -0700
    pointing users to other options to get our data in API docs, refs #34045
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    2ceb57ce1aad2e33d2521440fca156b5280f59a2 Fri Jul 5 11:30:15 2024 -0700
    clean up the revComp example refs #34045
  • lines changed 26, context: html, text, full: html, text
    720de849b76a5a3d95e66050d5a2c2683d60351a Fri Jul 5 12:58:50 2024 -0700
    adding list/genarkGenomes endpoint and examples refs #34045
  • lines changed 12, context: html, text, full: html, text
    faf3198f3682f6d9a999bc62908520fa2455ce0d Fri Jul 5 13:21:26 2024 -0700
    list/genarkGenomes is no out public yet refs #34045
  • lines changed 47, context: html, text, full: html, text
    c8ce6b749afee2a94df5a0b06fd79a8f29e33b44 Fri Jul 5 16:27:26 2024 -0700
    Adding a conditions of use to the hubApi documentation page, refs #32003. Making edits to Max's 'why not to use the API' section, refs #34072
• src/hg/htdocs/goldenPath/help/chain.html
  • lines changed 1, context: html, text, full: html, text
    603432fcd02e9d507270d670c266880895ce70ea Fri Jun 21 16:07:38 2024 -0700
    No redmine, noticed this randomly when going through docs
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 13, context: html, text, full: html, text
    32df51bb0c13175b852fe149d7514bb3c3eb0fb8 Wed Jul 3 10:11:15 2024 -0700
    Incorporating Lou's feedback for the adding groups to a track hub documentation, refs #33580
  • lines changed 4, context: html, text, full: html, text
    ae75856d0e07fd6964347b78b2e827e4f90b545e Fri Jul 5 14:16:02 2024 -0700
    hubClone the EPD Viewer Hub and updated the URLs to the goldenPath hubExamples, refs #34050
• src/hg/htdocs/images/epdHubEx.png
  • lines changed 0, context: html, text, full: html, text
    f9437315c865604186a3281d8fe4f254563a259f Tue Jul 2 16:23:34 2024 -0700
    Adding images for the adding groups to a track hub documentation, refs #33580
• src/hg/htdocs/images/epdHubGroups.png
  • lines changed 0, context: html, text, full: html, text
    f9437315c865604186a3281d8fe4f254563a259f Tue Jul 2 16:23:34 2024 -0700
    Adding images for the adding groups to a track hub documentation, refs #33580
• src/hg/htdocs/images/epdHub_Groups.png
  • lines changed 0, context: html, text, full: html, text
    32df51bb0c13175b852fe149d7514bb3c3eb0fb8 Wed Jul 3 10:11:15 2024 -0700
    Incorporating Lou's feedback for the adding groups to a track hub documentation, refs #33580
• src/hg/htdocs/indexMeetings.html
  • lines changed 15, context: html, text, full: html, text
    fd746abd8b4246b2f7ed2a8790f2e29955fdd3f4 Mon Jul 1 11:11:52 2024 -0700
    Missing a div tag, needed a wider screen to see issue
• src/hg/htdocs/style/HGStyle.css
  • lines changed 10, context: html, text, full: html, text
    d5783cef7d27b9f734131828ea4af40850e35d94 Mon Jul 1 15:52:26 2024 -0700
    hgc on hgTracks changes: 1: clicks outside of the pop up close the pop up. 2: item details is now in parens. 3: link to open in a new window is in an icon on the top right near the close icon. 4: Bottom button now just says close instead of ok, refs #33216
  • lines changed 1, context: html, text, full: html, text
    eb46c5c609a428f18202c6518ae97f5642e048e5 Tue Jul 2 11:34:22 2024 -0700
    Change open in new window icon on hgTracks hgc pop up to match the hgBlat open in new window icon, refs #33216
• src/hg/hubApi/apiUtils.c
  • lines changed 24, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/hubApi/dataApi.h
  • lines changed 12, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/hubApi/genomePriority.py
  • lines changed 174, context: html, text, full: html, text
    aff75303759349db45579315630cb17e9370f86f Fri Jul 5 16:07:27 2024 -0700
    now with assembly exist signal and including all RefSeq potential assemblies refs #32897
• src/hg/hubApi/getData.c
  • lines changed 4, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/hubApi/list.c
  • lines changed 12, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/hubApi/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/inc/genark.h
  • lines changed 14, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/js/hgTracks.js
  • lines changed 15, context: html, text, full: html, text
    d5783cef7d27b9f734131828ea4af40850e35d94 Mon Jul 1 15:52:26 2024 -0700
    hgc on hgTracks changes: 1: clicks outside of the pop up close the pop up. 2: item details is now in parens. 3: link to open in a new window is in an icon on the top right near the close icon. 4: Bottom button now just says close instead of ok, refs #33216
  • lines changed 1, context: html, text, full: html, text
    eb46c5c609a428f18202c6518ae97f5642e048e5 Tue Jul 2 11:34:22 2024 -0700
    Change open in new window icon on hgTracks hgc pop up to match the hgBlat open in new window icon, refs #33216
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    6c2d7c1b83c8d6155ea77aa76bae0d06c3720ceb Wed Jul 3 09:34:03 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/lib/chromAlias.c
  • lines changed 2, context: html, text, full: html, text
    532a820d6421a92ae969b83f0e267f60fae125b0 Mon Jul 1 14:14:54 2024 -0700
    check for /gbdb values for remapping for curated track hubs
• src/hg/lib/customFactory.c
  • lines changed 15, context: html, text, full: html, text
    9f9d1239c2d8e95152e9b637b52e7c77d88e4353 Tue Jul 2 09:16:40 2024 -0700
    add fancy settings to custom bigPsl tracks if none of them are already set refs #31304
  • lines changed 1, context: html, text, full: html, text
    81e77e54a305e8877679f1b4bb079f08755f479c Thu Jul 4 15:09:54 2024 -0700
    don't set mismatch options for all bigBeds, only bigPsl... d'oh
• src/hg/lib/genark.c
  • lines changed 38, context: html, text, full: html, text
    ba87d8471c9c78f15412ccad2aaba9b46d1af38e Tue Jul 2 16:14:47 2024 -0700
    eliminte the dependency upon specific genArk genome names, use the genark table for questions about existence, refs #32596
• src/hg/lib/genomePriority.h
  • lines changed 86, context: html, text, full: html, text
    634e8dd27316b349bb645e28095654c94c61c0f9 Fri Jul 5 13:33:17 2024 -0700
    incorrect location for this file refs #32897
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    532a820d6421a92ae969b83f0e267f60fae125b0 Mon Jul 1 14:14:54 2024 -0700
    check for /gbdb values for remapping for curated track hubs
  • lines changed 4, context: html, text, full: html, text
    93cffa046ab7bc81e9d3310c09d46f4de4f3d4b3 Wed Jul 3 10:53:11 2024 -0700
    defaultIsClosed is not a required group.txt setting
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 109, context: html, text, full: html, text
    7d22b62315f1138f347ff4e720f67658ca8426d3 Mon Jul 1 15:27:30 2024 -0700
    correct clade notations refs #29545
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    d217e9d5f944cdd45286c32aad912844d0f285fe Thu Jul 4 19:42:31 2024 -0700
    adding 2 per user request refs #29545
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    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    d217e9d5f944cdd45286c32aad912844d0f285fe Thu Jul 4 19:42:31 2024 -0700
    adding 2 per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    dbf63c8017a7942b2cadbafa74b4c684af36db26 Fri Jul 5 09:19:43 2024 -0700
    GenArk RefSeq update refs #29545
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cec4bfab74f738400696c0c191fe712fa33b997e Tue Jul 2 14:04:51 2024 -0700
    Adding release tags to the cartVersion 4 changes.
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    64f7632b2ea40aef3ae56c2249a8d9f11d7f6ad0 Sat Jul 6 13:03:42 2024 -0700
    Updating the mouseOver text for gnomad v4.1, refs #33746
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.alpha.ra
  • lines changed 75, context: html, text, full: html, text
    96ad7e779715f07a35732ba6c5168bd6413edc51 Tue Jul 2 13:03:45 2024 -0700
    enable sequence logos on catus 241 way
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    96ad7e779715f07a35732ba6c5168bd6413edc51 Tue Jul 2 13:03:45 2024 -0700
    enable sequence logos on catus 241 way
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    cec4bfab74f738400696c0c191fe712fa33b997e Tue Jul 2 14:04:51 2024 -0700
    Adding release tags to the cartVersion 4 changes.
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    5a5440cbd45e301bc1dd65ace81ff16e30981a2c Wed Jul 3 13:41:58 2024 -0700
    Accidentally messed up the tags, added two public.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cec4bfab74f738400696c0c191fe712fa33b997e Tue Jul 2 14:04:51 2024 -0700
    Adding release tags to the cartVersion 4 changes.
• src/hg/makeDb/trackDb/trackDb.mgc-orfeome.alpha.ra
  • lines changed 55, context: html, text, full: html, text
    cec4bfab74f738400696c0c191fe712fa33b997e Tue Jul 2 14:04:51 2024 -0700
    Adding release tags to the cartVersion 4 changes.
• src/hg/makeDb/trackDb/trackDb.mgc-orfeome.ra
  • lines changed 1, context: html, text, full: html, text
    cec4bfab74f738400696c0c191fe712fa33b997e Tue Jul 2 14:04:51 2024 -0700
    Adding release tags to the cartVersion 4 changes.
• src/utils/qa/assemblyStatsCron.py
  • lines changed 7, context: html, text, full: html, text
    1f929ead8ac83586b318b169e58509c181341276 Fri Jul 5 13:38:34 2024 -0700
    Changing location of tabFmt script which was moved.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    83c1707cf3712c5ed0a0920780f3a6e28e781cc4 Mon Jul 8 10:09:53 2024 -0700
    v468 preview2, refs #34044

• lines changed: 941
• files changed: 55