All File Changes

v482_preview2 to v482_base (2025-05-13 to 2025-05-19) v482

• confs/asia.hg.conf
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    052a4cfd598bede79c6a8b40b8b6e05ea226add3 Sun May 18 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    052a4cfd598bede79c6a8b40b8b6e05ea226add3 Sun May 18 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    052a4cfd598bede79c6a8b40b8b6e05ea226add3 Sun May 18 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    052a4cfd598bede79c6a8b40b8b6e05ea226add3 Sun May 18 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    052a4cfd598bede79c6a8b40b8b6e05ea226add3 Sun May 18 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• docs/gatewayTutorial.md
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    3400f3754a96dc0bf52ee14a4839fb0abac26d20 Mon May 19 09:12:32 2025 -0700
    Updating location for images and the interactive tutorial url, refs #34938
• docs/makefile
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    d48e737310b50372263fd683a2195fbaac6e0463 Wed May 14 09:01:22 2025 -0700
    adding alpha and beta targets for markdown makefile, refs #30335
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    63d21e7742dc1f41587536cb63881fae07a768ff Wed May 14 09:32:32 2025 -0700
    use pattern rules for running pandoc
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    3800922e51ee132e5c2df0773bdbaa9094a59909 Wed May 14 21:20:46 2025 -0700
    avoid permission errors when changing mode by using a tmp file
• src/hg/cgilib/bedCart.c
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    c54077c4044387203d4dc51151f54ad43854957a Thu May 15 14:30:46 2025 -0700
    changes in response to code review #35737
• src/hg/hgGateway/hgGateway.c
  • lines changed 5, context: html, text, full: html, text
    174d30f5d63b5c167a5af0457d1901a9620ec573 Tue May 13 16:50:29 2025 -0700
    Adding the Gateway and Table Browser tutorials to the Interactive Tutorial popup. Also adding the Help menu link to open the popup on the Gateway and Table Browser pages. Renaming the popup file to something more generic since it is no longer exclusive to hgTracks. Updating the makefile for the popup name change. refs #35716
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 7, context: html, text, full: html, text
    26754e1af309a8b7c47a44f22a114421d3da003b Wed May 14 16:18:19 2025 -0700
    Improving the new hubConnect redirect page with more information, a link to connect another hub, a disclaimer, and a temporary note that is more visually captivating to make sure users don't wait for the automatic refresh. Refs #29899
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    6a4153496eac6a158f48f5c3972f2c33ff37b7d0 Mon May 19 08:37:52 2025 -0700
    last minute wording changes to hub connect page, refs #29899
• src/hg/hgTables/mainPage.c
  • lines changed 31, context: html, text, full: html, text
    174d30f5d63b5c167a5af0457d1901a9620ec573 Tue May 13 16:50:29 2025 -0700
    Adding the Gateway and Table Browser tutorials to the Interactive Tutorial popup. Also adding the Help menu link to open the popup on the Gateway and Table Browser pages. Renaming the popup file to something more generic since it is no longer exclusive to hgTracks. Updating the makefile for the popup name change. refs #35716
• src/hg/hgTracks/bamTrack.c
  • lines changed 2, context: html, text, full: html, text
    bf04f597aad5ac68a705cf70312e0412d62aba0a Fri May 16 14:20:11 2025 -0700
    Updating the yellow bar message when too many items in display, refs #35330
• src/hg/hgTracks/simpleTracks.c
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    f05591924162fab32f39837b62ee866b5826eb9b Wed May 14 09:41:31 2025 -0700
    increase the size of a buffer used for exon phases etc.
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    508c37ee710797d32c6981c9227db6fa388dc304 Thu May 15 10:37:12 2025 -0700
    fixed buffer overflow in fixed size mouseover buffer
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    6653939f865225a4141f5b2a1b970e34b92b1226 Fri May 16 08:23:59 2025 -0700
    fixing right-click ID for gene pred tracks, refs #35756
  • lines changed 2, context: html, text, full: html, text
    677dcea9305f7851a04cc8d7204479ffa8e0554c Fri May 16 08:46:02 2025 -0700
    fixing right-click exon options for gene pred tracks, refs #35756
  • lines changed 1, context: html, text, full: html, text
    9b8908e274094a80d7e011fa3bd2f603ab563732 Fri May 16 11:20:33 2025 -0700
    tiny docs change, refs #33749
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    87e3dd1dc9e6c04c583502892c941eaf5b1e34b6 Sat May 17 09:05:40 2025 -0700
    fix a problem created by making tvShow a separate enum instead of an alias for tvFull. refs #35753
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    3d13f35406b44301ef87f8f01606b1801163cc7f Mon May 19 06:34:00 2025 -0700
    adding note that user needs to zoom in more to show cdna positions on exon mouseover, refs #35759
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    7d86d32d1dd31afc7508edb2ee157a583cc5e6e3 Mon May 19 06:46:24 2025 -0700
    improve exon mouseover for genePreds after feedback from QA, refs #33749
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    822ba4b1f1e9c734a0c6ebc19f2b3c0233063746 Wed May 14 14:52:01 2025 -0700
    Fix readonly blat input sequences, found by QA. refs #32750
  • lines changed 1, context: html, text, full: html, text
    63164243390df77a62fd47d5aeafbe01444576be Thu May 15 11:42:51 2025 -0700
    Fixes bug found by QA for show ali in window link refs #32750
• src/hg/htdocs/assemblyRequest.html
  • lines changed 10, context: html, text, full: html, text
    d6861d8f0eb72ab5fd3b940f25193934101e7033 Fri May 16 10:58:13 2025 -0700
    redirect page for this obsolete function to the new search page refs #32596
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 49, context: html, text, full: html, text
    0497d2117545f7ce8b6caaf452c9b1e10dbc2ed4 Fri May 16 10:45:34 2025 -0700
    News release for the pext track and the exon relevance RTS, refs #35116
• src/hg/htdocs/images/exonRelevanceNewsImage.png
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    0497d2117545f7ce8b6caaf452c9b1e10dbc2ed4 Fri May 16 10:45:34 2025 -0700
    News release for the pext track and the exon relevance RTS, refs #35116
• src/hg/htdocs/images/hg38pextTrackNewsImage.png
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    0497d2117545f7ce8b6caaf452c9b1e10dbc2ed4 Fri May 16 10:45:34 2025 -0700
    News release for the pext track and the exon relevance RTS, refs #35116
• src/hg/htdocs/images/tutorialImages/assemblyDetails.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/assemblyRequest.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/assemblyVersion.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/gatewayPageAnnotated.jpg
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/popularSpecies.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/requestPage.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/searchBox.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/sequencesList.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/speciesTree.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/images/tutorialImages/viewSequence.png
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    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 1, context: html, text, full: html, text
    0d81d059d480624c5481e7b54885dbc262a3ac80 Fri May 16 10:29:08 2025 -0700
    Adding new exon relevance RTS, refs #35725
• src/hg/htdocs/inc/recTrackSets.hg38.tab
  • lines changed 2, context: html, text, full: html, text
    0d81d059d480624c5481e7b54885dbc262a3ac80 Fri May 16 10:29:08 2025 -0700
    Adding new exon relevance RTS, refs #35725
• src/hg/htdocs/indexMeetings.html
  • lines changed 26, context: html, text, full: html, text
    76b5d02229ecfef4e7851e2c7d76c821c688b192 Fri May 16 12:14:35 2025 -0700
    Updating meetings page to remove meetings that have passed, and updating with upcoming ones.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    0497d2117545f7ce8b6caaf452c9b1e10dbc2ed4 Fri May 16 10:45:34 2025 -0700
    News release for the pext track and the exon relevance RTS, refs #35116
• src/hg/htdocs/robots.rr.txt
  • lines changed 2, context: html, text, full: html, text
    1bcf1f9b2eb137504e27f48cdf26b983106fecf3 Wed May 14 09:29:43 2025 -0700
    removing bytedance bot, no redmine
  • lines changed 3, context: html, text, full: html, text
    42d5350916ba1097d55cc7223c35431536fc0e93 Wed May 14 12:32:38 2025 -0700
    Bytespider was listed twice, also made them alphabetical.
• src/hg/inc/versionInfo.h
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    e4481bfc920729522f59d98b7fdfd09023e9ce4f Mon May 19 11:24:48 2025 -0700
    New version number v482
• src/hg/js/hgGateway.js
  • lines changed 22, context: html, text, full: html, text
    174d30f5d63b5c167a5af0457d1901a9620ec573 Tue May 13 16:50:29 2025 -0700
    Adding the Gateway and Table Browser tutorials to the Interactive Tutorial popup. Also adding the Help menu link to open the popup on the Gateway and Table Browser pages. Renaming the popup file to something more generic since it is no longer exclusive to hgTracks. Updating the makefile for the popup name change. refs #35716
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    bc0e542145aaf30eac158430d9336441f632ba26 Tue May 13 16:41:24 2025 -0700
    Fixing a small typo in the href (tutorial is misspelled), refs #35716
  • lines changed 5, context: html, text, full: html, text
    0983285caec2469eeb7e50ec22fe8042afefa900 Thu May 15 14:00:45 2025 -0700
    Breaking message over multiple lines, feedback from CR. Refs #35746
  • lines changed 18, context: html, text, full: html, text
    6653939f865225a4141f5b2a1b970e34b92b1226 Fri May 16 08:23:59 2025 -0700
    fixing right-click ID for gene pred tracks, refs #35756
  • lines changed 26, context: html, text, full: html, text
    677dcea9305f7851a04cc8d7204479ffa8e0554c Fri May 16 08:46:02 2025 -0700
    fixing right-click exon options for gene pred tracks, refs #35756
  • lines changed 13, context: html, text, full: html, text
    c377d3a1c3cd62fc18f152243a162c8e718e7e88 Fri May 16 16:32:06 2025 -0700
    Adds Right-click Track Description feature in hgTracks.js. fixes 31584
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    3ca4af9ada5ba351b0edb9ec68032b9e7bf4f1cd Fri May 16 16:36:54 2025 -0700
    Oops removing debug warning.
• src/hg/js/tutorials/gatewayTutorial.js
  • lines changed 5, context: html, text, full: html, text
    eb68b3a135155c434e421033b8d1f70bcfa86111 Fri May 16 19:11:09 2025 -0700
    Moving Gateway tutorial images to tutorialImages directory and updating gatewayTutorial.js to reflect change, refs #35464
• src/hg/js/tutorials/makefile
  • lines changed 1, context: html, text, full: html, text
    174d30f5d63b5c167a5af0457d1901a9620ec573 Tue May 13 16:50:29 2025 -0700
    Adding the Gateway and Table Browser tutorials to the Interactive Tutorial popup. Also adding the Help menu link to open the popup on the Gateway and Table Browser pages. Renaming the popup file to something more generic since it is no longer exclusive to hgTracks. Updating the makefile for the popup name change. refs #35716
• src/hg/js/tutorials/tableBrowserTutorial.js
  • lines changed 3, context: html, text, full: html, text
    f82364f0da73f6347b25a171b3f4845e87694e1c Thu May 15 17:01:27 2025 -0700
    Removing the last line about sending information to Galaxy or GREAT, refs #35126
• src/hg/js/tutorials/tutorialPopup.js
  • lines changed 56, context: html, text, full: html, text
    174d30f5d63b5c167a5af0457d1901a9620ec573 Tue May 13 16:50:29 2025 -0700
    Adding the Gateway and Table Browser tutorials to the Interactive Tutorial popup. Also adding the Help menu link to open the popup on the Gateway and Table Browser pages. Renaming the popup file to something more generic since it is no longer exclusive to hgTracks. Updating the makefile for the popup name change. refs #35716
  • lines changed 4, context: html, text, full: html, text
    854a0dd63ee7b737f0273f9329707111774f8d4b Wed May 14 13:57:39 2025 -0700
    Edits to the Gateway section of the interactive tutorials dropdown, refs #35716
• src/hg/lib/trackDbCustom.c
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    c54077c4044387203d4dc51151f54ad43854957a Thu May 15 14:30:46 2025 -0700
    changes in response to code review #35737
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    a2b64b9d2358a5e6ec6c6dbfac102bd78fb27663 Tue May 13 16:03:08 2025 -0700
    adding one per user request refs #29545
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    5c843d25210930c1fd699e23f1632cf2b6b25067 Wed May 14 11:04:21 2025 -0700
    adding one per user request refs #29545
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    170c79270978a2686a58e91657412b99596299e5 Fri May 16 10:40:23 2025 -0700
    adding one per user request refs #34337
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 21, context: html, text, full: html, text
    cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
    implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 5, context: html, text, full: html, text
    1c297cf2b02d635690955ac09b5a915a7b8e54d5 Wed May 14 12:07:41 2025 -0700
    write out an information file about which assemblies have chain/net tracks "hasChainNets.txt" refs #34917
  • lines changed 97, context: html, text, full: html, text
    8859fbf8a8d7408df039c9ab29c8b3bdeb225516 Wed May 14 12:09:07 2025 -0700
    now writing out beta.hub.txt and public.hub.txt based on control from trackDb listings publicGenArk.txt and betaGenArk.txt refs #34917
  • lines changed 2, context: html, text, full: html, text
    f4cc4c7a53b4b1c33e5f83bc7e82b5145e7971b6 Thu May 15 13:33:45 2025 -0700
    correct blank lines in track stanzas in the public and beta hub.txt files refs #34917
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 33, context: html, text, full: html, text
    cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
    implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
• src/hg/makeDb/doc/asmHubs/sciNameOverride.txt
  • lines changed 22, context: html, text, full: html, text
    cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
    implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 21, context: html, text, full: html, text
    cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
    implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 1, context: html, text, full: html, text
    b6b05dad3475c3c668e83e70968380be5c767daf Fri May 16 10:39:43 2025 -0700
    new low track count for BRC project refs #34337
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 197, context: html, text, full: html, text
    e9ab99078ff5a3b1d8bc80002ed57f6400c3ec51 Fri May 16 07:17:04 2025 -0700
    catching up to BRC project list refs #34337
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 38, context: html, text, full: html, text
    b4fd34e71f94b2847253ef2b20cd3d8aa2acaa24 Mon May 19 10:31:30 2025 -0700
    Fix a few issues with MaveDB json parse (score bounds, item count display for cells with multiple values. Also committing trackDb and doc for a native version, refs #31812
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    5c843d25210930c1fd699e23f1632cf2b6b25067 Wed May 14 11:04:21 2025 -0700
    adding one per user request refs #29545
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    fd2acb99619aee5e48bd79c9de487b43236079f2 Thu May 15 13:46:54 2025 -0700
    correct common names on the F1 haploid assemblies refs #34370
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    b38b615425ec779eb4fdb2135fe34c8cc6b8c9ad Thu May 15 15:21:07 2025 -0700
    common name fixups to match VGP listings refs 34370
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    170c79270978a2686a58e91657412b99596299e5 Fri May 16 10:40:23 2025 -0700
    adding one per user request refs #34337
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    fd2acb99619aee5e48bd79c9de487b43236079f2 Thu May 15 13:46:54 2025 -0700
    correct common names on the F1 haploid assemblies refs #34370
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a2b64b9d2358a5e6ec6c6dbfac102bd78fb27663 Tue May 13 16:03:08 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    c2a768a6f781c36cc2fcfff8f59da94b021ac7d6 Thu May 15 15:11:22 2025 -0700
    common name fixups to match VGP listings refs 34370
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    6f8f116800e9cfef3f3f80883a8d0690bedaa556 Thu May 15 15:24:13 2025 -0700
    common name fixups to match VGP listings refs 34370
• src/hg/makeDb/trackDb/betaGenArk.txt
  • lines changed 4, context: html, text, full: html, text
    ed2e2fa8c95fd33065539210e89cc7decb12998f Wed May 14 12:02:09 2025 -0700
    adding genark beta and public track control listings refs #34917
• src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html
  • lines changed 11, context: html, text, full: html, text
    f86d097e1dac55d91a23830697808108abad9a00 Thu May 15 13:28:01 2025 -0700
    html and trackDb for contributed Tiberius gene tracks refs #34917
• src/hg/makeDb/trackDb/contrib/tiberius/tiberius.trackDb.txt
  • lines changed 12, context: html, text, full: html, text
    f86d097e1dac55d91a23830697808108abad9a00 Thu May 15 13:28:01 2025 -0700
    html and trackDb for contributed Tiberius gene tracks refs #34917
• src/hg/makeDb/trackDb/human/clinvar.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    5fcd812cf1a00e161e4fa07c34f989dac1dbc624 Wed May 14 08:10:42 2025 -0700
    adding clinvar decorator to alpha trackDb, refs #35750
• src/hg/makeDb/trackDb/human/clinvar.ra
  • lines changed 4, context: html, text, full: html, text
    9e36613d3d880b010ebfd410b144a3f6995d211e Tue May 13 16:14:39 2025 -0700
    Adding filter capabilities to the clinvar track so we can configure the exon RTS, refs #35725
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
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    e7a1391bd9ac64eec29a4f06d27f70adc789a659 Fri May 16 10:07:13 2025 -0700
    Staging the GENCODE Genes tracks for human and mouse on the RR, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    980980951bd7c128c27870a376cba9f6d820e58a Thu May 15 17:00:31 2025 -0700
    Staging the GENCODE Genes track for hg38, hg19, and mm39 on hgwbeta, refs #35186 #35187 #35189
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    e7a1391bd9ac64eec29a4f06d27f70adc789a659 Fri May 16 10:07:13 2025 -0700
    Staging the GENCODE Genes tracks for human and mouse on the RR, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/human/hg38/gnomad.pext.ra
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    a07b191d55246458860278d9006bb45a232c90f3 Tue May 13 16:12:12 2025 -0700
    Staging the hg38 gnomAD pext track, refs #35116
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    5b38b32ab18c6dc6124d36645af4b8b39db9cf77 Tue May 13 16:26:23 2025 -0700
    Hiding by default and adding pennantIcon to the superTrack, refs #35116
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    a2da2b6bdfd0baa55331fbf759c1bffae0b80faf Tue May 13 16:49:14 2025 -0700
    Adding pennantIcon to the superTrack, refs #35116
• src/hg/makeDb/trackDb/human/hg38/gnomadPext.html
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    a07b191d55246458860278d9006bb45a232c90f3 Tue May 13 16:12:12 2025 -0700
    Staging the hg38 gnomAD pext track, refs #35116
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    a1d7abb1b3ff06ae5ad1b75d38abeb125e636b02 Wed May 14 17:52:26 2025 -0700
    Updating the desc page to say 50 tissues as opposed to the 53 from hg19. Refs #35116
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    e7a1391bd9ac64eec29a4f06d27f70adc789a659 Fri May 16 10:07:13 2025 -0700
    Staging the GENCODE Genes tracks for human and mouse on the RR, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/human/hg38/mavedb.ra
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    b4fd34e71f94b2847253ef2b20cd3d8aa2acaa24 Mon May 19 10:31:30 2025 -0700
    Fix a few issues with MaveDB json parse (score bounds, item count display for cells with multiple values. Also committing trackDb and doc for a native version, refs #31812
• src/hg/makeDb/trackDb/human/hg38/mavedb_maps.html
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    b4fd34e71f94b2847253ef2b20cd3d8aa2acaa24 Mon May 19 10:31:30 2025 -0700
    Fix a few issues with MaveDB json parse (score bounds, item count display for cells with multiple values. Also committing trackDb and doc for a native version, refs #31812
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.html
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    0ea0a81ddc0fe93a9a7b4edcc4c09060f3187c7f Mon May 19 10:40:54 2025 -0700
    Code review edits and releasing the updated Pseudogenes track, refs #35741
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.new.html
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    bdbac0c65d02f6a46a0723d88cb7a2fe7a0e3ba0 Thu May 15 17:00:38 2025 -0700
    Code review edits, refs #35741
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
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    fb4c73b0577b4057cbaee475ee42c50a263b64fd Thu May 15 16:22:13 2025 -0700
    Changing to a tiny useless summary file so that the track loads quickly on large regions. Previously it could stall browsers for 10-30 seconds on big regions if the track was on. Refs #35534
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    a07b191d55246458860278d9006bb45a232c90f3 Tue May 13 16:12:12 2025 -0700
    Staging the hg38 gnomAD pext track, refs #35116
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    980980951bd7c128c27870a376cba9f6d820e58a Thu May 15 17:00:31 2025 -0700
    Staging the GENCODE Genes track for hg38, hg19, and mm39 on hgwbeta, refs #35186 #35187 #35189
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    e7a1391bd9ac64eec29a4f06d27f70adc789a659 Fri May 16 10:07:13 2025 -0700
    Staging the GENCODE Genes tracks for human and mouse on the RR, refs #35186 #35187 #35189
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    b4fd34e71f94b2847253ef2b20cd3d8aa2acaa24 Mon May 19 10:31:30 2025 -0700
    Fix a few issues with MaveDB json parse (score bounds, item count display for cells with multiple values. Also committing trackDb and doc for a native version, refs #31812
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    0ea0a81ddc0fe93a9a7b4edcc4c09060f3187c7f Mon May 19 10:40:54 2025 -0700
    Code review edits and releasing the updated Pseudogenes track, refs #35741
• src/hg/makeDb/trackDb/human/linsight.ra
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    7a43f074ea93fdbf0bb7e427e5ed1d8c8bda0821 Tue May 13 13:12:11 2025 -0700
    Adding .ra file that Max had forgotten to commit, refs #35730
• src/hg/makeDb/trackDb/human/nmdEscape.ra
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    09c6f376e185d8cceb98aeb0f3b6faec374e6bce Fri May 16 07:53:18 2025 -0700
    adding back nmdEscape track, email from Lou
• src/hg/makeDb/trackDb/human/trackDb.ra
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    8448928dc812afc19495fbb51701c51028af6d82 Tue May 13 04:57:00 2025 -0700
    adding nmd escape track, not in redmine yet
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    07c8f583536331be74f4ceaf8d11bd57b5318f35 Wed May 14 01:26:20 2025 -0700
    Added hgnc symbol to mouseover
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    85cac5cc60514c9fb5a01a50536fc01c161978dd Thu May 15 16:20:50 2025 -0700
    Revert "adding nmd escape track, not in redmine yet" This reverts commit 8448928dc812afc19495fbb51701c51028af6d82. This is because we have a missing nmd.ra file so it breaks the human tdb builds.
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    09c6f376e185d8cceb98aeb0f3b6faec374e6bce Fri May 16 07:53:18 2025 -0700
    adding back nmdEscape track, email from Lou
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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    e7a1391bd9ac64eec29a4f06d27f70adc789a659 Fri May 16 10:07:13 2025 -0700
    Staging the GENCODE Genes tracks for human and mouse on the RR, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    980980951bd7c128c27870a376cba9f6d820e58a Thu May 15 17:00:31 2025 -0700
    Staging the GENCODE Genes track for hg38, hg19, and mm39 on hgwbeta, refs #35186 #35187 #35189
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    e7a1391bd9ac64eec29a4f06d27f70adc789a659 Fri May 16 10:07:13 2025 -0700
    Staging the GENCODE Genes tracks for human and mouse on the RR, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/publicGenArk.txt
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    ed2e2fa8c95fd33065539210e89cc7decb12998f Wed May 14 12:02:09 2025 -0700
    adding genark beta and public track control listings refs #34917
• src/hg/makeDb/trackDb/tagTypes.tab
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    b4fd34e71f94b2847253ef2b20cd3d8aa2acaa24 Mon May 19 10:31:30 2025 -0700
    Fix a few issues with MaveDB json parse (score bounds, item count display for cells with multiple values. Also committing trackDb and doc for a native version, refs #31812
• src/hg/oneShot/parseMave/parseMave.pl
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    b4fd34e71f94b2847253ef2b20cd3d8aa2acaa24 Mon May 19 10:31:30 2025 -0700
    Fix a few issues with MaveDB json parse (score bounds, item count display for cells with multiple values. Also committing trackDb and doc for a native version, refs #31812
• src/hg/utils/otto/genArk/alphaBetaPush.pl
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    5ee6a100c664a51ff24ae10ae7779bbe3b506603 Wed May 14 15:31:08 2025 -0700
    now managing the push of beta and public versions of hub.txt files for contrib tracks in genark browsers refs #34917
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    f35500dabcf4527f5a1a482d4e0da03c44f01f63 Thu May 15 14:03:05 2025 -0700
    correctly rsync only in the case where the contrib/track directory does actually exist refs #35917
• src/hg/utils/otto/genArk/pushRR.sh
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    5ee6a100c664a51ff24ae10ae7779bbe3b506603 Wed May 14 15:31:08 2025 -0700
    now managing the push of beta and public versions of hub.txt files for contrib tracks in genark browsers refs #34917
• src/hg/utils/otto/panelApp/cnv.py
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    11a7d1aac16cfc653302a713b756fe4c352f450d Mon May 19 02:34:40 2025 -0700
    fixing panelApp bug, refs #35757
• src/hg/utils/otto/panelApp/tandRep.py
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    11a7d1aac16cfc653302a713b756fe4c352f450d Mon May 19 02:34:40 2025 -0700
    fixing panelApp bug, refs #35757
• src/inc/srcVersion.h
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    e4481bfc920729522f59d98b7fdfd09023e9ce4f Mon May 19 11:24:48 2025 -0700
    New version number v482
• src/utils/hubtools/hubtools
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    b37c3e0908d07a7fe62e8925f1ace13a5ccf91f1 Fri May 16 02:17:49 2025 -0700
    hubtools fix to avoid uploading a file that has already been uploaded
• src/utils/qa/weeklybld/buildEnv.csh
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    5712ed688eb5c2aff7db810744deee93dc0d6103 Mon May 19 11:24:14 2025 -0700
    v482 final build, refs #35666

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