All File Changes

v466_preview2 to v466_base (2024-05-27 to 2024-06-03) v466

• src/hg/hgPhyloPlace/phyloPlace.c
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    725e90237508115d42656743ea35a6da01be4464 Wed May 29 18:49:14 2024 -0700
    When multiple references are matched, we make multiple 'view single subtree' buttons so add serial number to their IDs to prevent broken clicks. Also, apply MAX_SUBTREE_BUTTONS only when we're making individual buttons, not when we're making a dropdown to select the subtree.
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    2a1ae24649f8f1bcc3cce498418597d88fb423e4 Fri May 31 04:55:37 2024 -0700
    moving to jsdelivr as a much faster CDN, we should stop using CDNs. Note that while this is 4.7, the major versions are compatible and the docs say they just added icons. refs #33817
• src/hg/hgc/bamClick.c
  • lines changed 16, context: html, text, full: html, text
    af401081fe03d2bd9eb087487939075d29ff8e03 Fri May 31 08:43:30 2024 -0700
    not showing bam query alignment if seq is too long, refs #33292
  • lines changed 44, context: html, text, full: html, text
    0345dae65cc819f447fb0414829b2f6d32473c32 Sun Jun 2 13:24:16 2024 -0700
    added number of start/end hard and soft based to BAM hgc page
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 13, context: html, text, full: html, text
    5251afff4391b653e4d352ea68fb06d10e99246f Fri May 31 07:32:51 2024 -0700
    adding extra fields to bigPsl docs, refs #17950
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    687a9c88647a46f71d40f2d04b77251b5a9cff55 Fri May 31 08:06:39 2024 -0700
    section docs, refs #17950
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    ac67c40af43801ce6a8bb6e7fe1beeb2b49fb355 Mon Jun 3 04:50:49 2024 -0700
    Adding a additional fields note for the bigPsl Track Format page, refs #17950
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
  • lines changed 28, context: html, text, full: html, text
    1cb7fc28305bae2eddf80c3f9b6cdb8b10ee3255 Thu May 30 01:05:27 2024 -0700
    adding notes about track hub stability, refs #33768;
  • lines changed 22, context: html, text, full: html, text
    da5bc480b8407f71f87c5c83f560ec7149ff7ec1 Mon Jun 3 03:23:07 2024 -0700
    Adding a note on stability for track hubs, refs #33768
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 1, context: html, text, full: html, text
    029a01f054a97bc5440b4f152ce2e8963cd47231 Fri May 31 22:36:10 2024 -0700
    Covering other copyright footer messages throughout the site, refs #33592
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    029a01f054a97bc5440b4f152ce2e8963cd47231 Fri May 31 22:36:10 2024 -0700
    Covering other copyright footer messages throughout the site, refs #33592
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 1, context: html, text, full: html, text
    1de21c7f6b33b73b57e806cd3f0532d180f4b975 Wed May 29 16:29:41 2024 -0700
    Updating footer copyright from 2022 to 2024 ref #33592
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 1, context: html, text, full: html, text
    029a01f054a97bc5440b4f152ce2e8963cd47231 Fri May 31 22:36:10 2024 -0700
    Covering other copyright footer messages throughout the site, refs #33592
• src/hg/htdocs/indexMeetings.html
  • lines changed 13, context: html, text, full: html, text
    20579007e6a333d4a5563f699b3149be95fbf74e Tue May 28 09:53:08 2024 -0700
    Adding new workshops
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    87b390a59ee5e4f3942b557b3a76eadf3ab1ca0d Mon Jun 3 10:43:03 2024 -0700
    New version number v466
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    555f22a0e1f02c1f07d98a0cb0906a152748295f Tue May 28 11:59:00 2024 -0700
    Fix input not being a part of its parent, #33769
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    500ffbd83571094d07113b37f4b116db159d29ad Wed May 29 17:24:31 2024 -0700
    Unencode dash characters so lookups into hgTracks.trackDb object still work, refs #33216.
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    fee8731474a2f55059bbe9c5da1b0bc01c0f8b41 Wed May 29 14:34:30 2024 -0700
    Don't bold search results in hgTables, refs #33731
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    db9adb6c99c75f8ec1076697ac965b2fb498c93b Wed May 29 16:14:01 2024 -0700
    Removing break ruler tags, ref #33578
• src/hg/lib/quickLift.c
  • lines changed 4, context: html, text, full: html, text
    6f9be896e698affdeb0f5bc22369c0be69029048 Wed May 29 13:33:38 2024 -0700
    don't try to read data off the beginning of the chrom.
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 7, context: html, text, full: html, text
    abd40be98069342ad0281cdcb42c2298be33e1cb Thu May 30 09:46:50 2024 -0700
    special case some more invertebrate names refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    1ccb8ac66ce9d7f004751065aefd285737da1d9f Mon May 27 13:01:52 2024 -0700
    remove assembly never built not needed refs #29545
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    8b9c593a175ed7a8cb2fb69a810ba806e86721f9 Wed May 29 11:36:17 2024 -0700
    catching up master.run.list with tsv listings refs #29545
  • lines changed 151, context: html, text, full: html, text
    98c798121621aa4671ddad936a5a37ff2ac6c57a Thu May 30 12:26:17 2024 -0700
    refSeq update adding 151 assmblies refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 32, context: html, text, full: html, text
    eab19783dc8a751d40d5b1c6c7da81d10a7a4d99 Mon May 27 17:47:09 2024 -0700
    catching up completed builds refs #29545
  • lines changed 1, context: html, text, full: html, text
    1afa30fb96e679291e406c7143ef5d296fd7686a Tue May 28 20:08:20 2024 -0700
    GCA_000750555.1_ASM75055v1 is already in legacy refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 69, context: html, text, full: html, text
    53cf1f5a5e8202b5358beabdb42287776c717595 Thu May 30 11:42:03 2024 -0700
    refSeq update adding 20 assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 75, context: html, text, full: html, text
    2727be6ec3249dd652f8527c491275414297c3b4 Thu May 30 11:37:08 2024 -0700
    refSeq update adding 23 assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 40, context: html, text, full: html, text
    32cbcfd8e5641b6562603e225a81fbe515731b61 Thu May 30 09:47:54 2024 -0700
    refSeq update adding 37 refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 5, context: html, text, full: html, text
    e12aafdc608e1d74cc36b6707f54299910e8b7fe Tue May 28 02:30:36 2024 -0700
    updating HGMD to 2023 version, refs #32001
• src/hg/makeDb/doc/hg38/hgmd.txt
  • lines changed 3, context: html, text, full: html, text
    e12aafdc608e1d74cc36b6707f54299910e8b7fe Tue May 28 02:30:36 2024 -0700
    updating HGMD to 2023 version, refs #32001
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 4, context: html, text, full: html, text
    e12aafdc608e1d74cc36b6707f54299910e8b7fe Tue May 28 02:30:36 2024 -0700
    updating HGMD to 2023 version, refs #32001
• src/hg/makeDb/doc/hg38/spliceAI.txt
  • lines changed 70, context: html, text, full: html, text
    f68839c12f3e1ad0fa4223d71782c1e2f509d10b Wed May 29 15:43:23 2024 -0700
    Bringing in and releases the SpliceAI data from the hub Jeltje made, refs #27141
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    ef367b73c79c5ad168ead9ad42cd384a1c4e6452 Wed May 29 12:54:42 2024 -0700
    catching up tsv list with master.run.list refs #29545
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    104dfe4740b3363b058a8d5e983ed56848c7cb0b Thu May 30 11:18:11 2024 -0700
    RefSeq update adding 34 assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    1c4294c39020e784e893810c63c42031a754f132 Wed May 29 12:55:14 2024 -0700
    catching up tsv list with master.run.list refs #29545
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    47232476dfffb3b6d05e6a2f8c509dd84c15edb8 Thu May 30 12:29:05 2024 -0700
    refSeq update adding 12 assmblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 62, context: html, text, full: html, text
    7bfe0194d5fe28ee32472a45199ad0f5427fe795 Tue May 28 11:59:05 2024 -0700
    catching up to completed builds adding 32 sequences refs #29545
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    d4d7392ddf8074b036de308d83f6cd608e008cea Thu May 30 12:19:22 2024 -0700
    refSeq update adding 12 assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    760be579917b7fb47bf760b0850a318a64bb0afa Wed May 29 11:09:59 2024 -0700
    adding an Indian cobra per user requesr refs #29545
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    bbc6a6bd58f21079981d41c4b99c2ef6fb0c0647 Thu May 30 12:20:18 2024 -0700
    refSeq update adding 13 assemblies refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 230, context: html, text, full: html, text
    4e902ad3b9b51edc9fd753bd7f6a77bf978ad18f Tue May 28 11:57:44 2024 -0700
    catching up to completed builds adding 16 sequences refs #29545
• src/hg/makeDb/trackDb/human/abSplice.ra
  • lines changed 1, context: html, text, full: html, text
    ec7aef895bf6e1168c52dd5b43f136d22061f4d6 Mon May 27 12:52:29 2024 -0700
    Deleting the hg38 abSplice files since the hg38/hg19 abSplice files were combined into the human directory and updating the pennantIcon, refs #33251
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    026120ef528e6f1ec90cae0cfab94c155f506298 Tue May 28 05:25:09 2024 -0700
    adding note about decipher browser to hg19 gnomad constraint track, email from Lou to Guido, no redmine yet
• src/hg/makeDb/trackDb/human/hg38/abSplice.html
  • lines changed 77, context: html, text, full: html, text
    ec7aef895bf6e1168c52dd5b43f136d22061f4d6 Mon May 27 12:52:29 2024 -0700
    Deleting the hg38 abSplice files since the hg38/hg19 abSplice files were combined into the human directory and updating the pennantIcon, refs #33251
• src/hg/makeDb/trackDb/human/hg38/abSplice.ra
  • lines changed 16, context: html, text, full: html, text
    ec7aef895bf6e1168c52dd5b43f136d22061f4d6 Mon May 27 12:52:29 2024 -0700
    Deleting the hg38 abSplice files since the hg38/hg19 abSplice files were combined into the human directory and updating the pennantIcon, refs #33251
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f68839c12f3e1ad0fa4223d71782c1e2f509d10b Wed May 29 15:43:23 2024 -0700
    Bringing in and releases the SpliceAI data from the hub Jeltje made, refs #27141
• src/hg/makeDb/trackDb/human/spliceAI.html
  • lines changed 77, context: html, text, full: html, text
    092b1f6d8b05019906c903090236b8d7a3a59220 Wed May 29 16:04:16 2024 -0700
    Addin the desc page for the spliceAI track, refs #27141
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e12aafdc608e1d74cc36b6707f54299910e8b7fe Tue May 28 02:30:36 2024 -0700
    updating HGMD to 2023 version, refs #32001
  • lines changed 16, context: html, text, full: html, text
    f68839c12f3e1ad0fa4223d71782c1e2f509d10b Wed May 29 15:43:23 2024 -0700
    Bringing in and releases the SpliceAI data from the hub Jeltje made, refs #27141
• src/hg/utils/buildPairAssembly/buildPairAssembly.c
  • lines changed 56, context: html, text, full: html, text
    6f8a50068e6c1558dbbf286b9a573800c68b1fb1 Tue May 28 17:16:22 2024 -0700
    ongoing work on pair browser
• src/hg/utils/buildPairAssembly/makePair
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    6f8a50068e6c1558dbbf286b9a573800c68b1fb1 Tue May 28 17:16:22 2024 -0700
    ongoing work on pair browser
• src/inc/srcVersion.h
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    87b390a59ee5e4f3942b557b3a76eadf3ab1ca0d Mon Jun 3 10:43:03 2024 -0700
    New version number v466
• src/utils/qa/assemblyStatsCron.py
  • lines changed 110, context: html, text, full: html, text
    ba218fbf9fae129b38710a813d9d748f89f445fa Wed May 29 17:21:43 2024 -0700
    Fixing up the monthly usage stats cron. Major changes include converting to python from ipython, fixing issue where default tracks were not being filtered out, and now correctly identifies from which mirror all hubs come from, refs #26191
  • lines changed 5, context: html, text, full: html, text
    09f521bfbb529e43c5d33cb052c95851ae792d12 Mon Jun 3 08:47:55 2024 -0700
    Fixing an issue where the output wasn't being mailed when I swapped this script from ipython to python - the output needs to be printed.
• src/utils/qa/checkSessionsFromRR.py
  • lines changed 252, context: html, text, full: html, text
    6aab74a2672b23a62ef96216f4ab5c0189e3478f Mon May 27 13:57:19 2024 -0700
    Adding a script that gets user sessions that load on hgw0 then checks if the sessions load on hgwdev and hgwbeta to check if they crash, refs #32593
• src/utils/qa/makefile
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    c027de3333e990270cfa61c690b3f5107193620c Mon May 27 14:01:54 2024 -0700
    Adding a script to make a cron that gets user sessions that load on hgw0 then checks if the sessions load on hgwdev and hgwbeta to check if they crash, refs #32593
• src/utils/qa/qaTestScript.py
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    580812942ea6dcf06d1cff08b4e3603b6facc638 Wed May 29 12:35:39 2024 -0700
    Copied Brian's session and saved it to the QAtester session account. Copied Brian's links and Gerardo's links to the genecats directory. Changed the links for the script. No redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    1de4164a59603c354221d73a1422e502efba2d8e Mon Jun 3 10:35:44 2024 -0700
    v466 final build, refs #33762

• lines changed: 1758
• files changed: 59