All File Changes

v423_base to v424_preview (2021-11-09 to 2021-11-15) v424

• confs/hgwdev.hg.conf
  • lines changed 5, context: html, text, full: html, text
    9e1511cc08feb956852b37864db1c54ae9490f4d Sun Nov 14 01:11:50 2021 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgCustom/hgCustom.c
  • lines changed 54, context: html, text, full: html, text
    f3009e2f9d911795bd1d13a0f95bbbee46309f83 Sun Nov 14 18:54:39 2021 -0800
    Adding warn-and-continue option to hgCustom. Motivation is to support https warnings but will be useful more widely. refs #28458
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    124b93d91306e54dba9b2a30daffc129cf895af4 Thu Nov 11 11:07:33 2021 -0800
    Changing the share link to be relative, refs #28324
• src/hg/hgTracks/bigRmskTrack.c
  • lines changed 1681, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgTracks/simpleTracks.c
  • lines changed 7, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 17, context: html, text, full: html, text
    36650b61875fa047f2c9ebc3657d1a9d10ec77e6 Fri Nov 12 14:42:17 2021 -0800
    Give developers a way to map sequence names to labels in maf display refs #28495
• src/hg/hgTracks/wigTrack.c
  • lines changed 299, context: html, text, full: html, text
    b5c461e5c49abf9eb5a708e2b63243555b2362da Wed Nov 10 18:05:28 2021 -0800
    first cut at a sequence logo track, also some makeDoc for gene tracks
• src/hg/hgc/bigRmskClick.c
  • lines changed 368, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
  • lines changed 2, context: html, text, full: html, text
    36650b61875fa047f2c9ebc3657d1a9d10ec77e6 Fri Nov 12 14:42:17 2021 -0800
    Give developers a way to map sequence names to labels in maf display refs #28495
• src/hg/hgc/hgc.h
  • lines changed 1, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hgc/mafClick.c
  • lines changed 6, context: html, text, full: html, text
    36650b61875fa047f2c9ebc3657d1a9d10ec77e6 Fri Nov 12 14:42:17 2021 -0800
    Give developers a way to map sequence names to labels in maf display refs #28495
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/htdocs/covid19.html
  • lines changed 1, context: html, text, full: html, text
    81ef25bc67b201e37f2e008500e275c41bcc61d9 Mon Nov 15 09:04:50 2021 -0800
    Fixing a link found by monthly Static Page Cronjob
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 6, context: html, text, full: html, text
    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 12, context: html, text, full: html, text
    5b5ab5deac3d892d181614dc496156ad7b688d7e Wed Nov 10 17:03:59 2021 -0800
    Adding a note about invisible trackDb architecture caching and updating udcTimeout to 5 seconds from 1 second refs #28487
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 52, context: html, text, full: html, text
    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 208, context: html, text, full: html, text
    4738e2765fa6ddcd9025f53ddfc1da7bf8f68fb0 Tue Nov 9 08:38:00 2021 -0800
    Adding new section about release of scRNA-seq track group. refs #26964
  • lines changed 2, context: html, text, full: html, text
    0ea280eb8cb4163a81a84e9c09b72c49aa7de8d3 Tue Nov 9 09:32:02 2021 -0800
    Changing width of scRNA-seq track group image. refs #26964
  • lines changed 16, context: html, text, full: html, text
    abaf7f9f1b28276820f73cc81c067f9b4bae6814 Mon Nov 15 08:04:25 2021 -0800
    Edited release date for scRNA-seq track group. refs #28378
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    345463359677ddbd707af106bd2fa4d139f52013 Wed Nov 10 11:43:05 2021 -0800
    Adding accent to Anna's last name to match in on publication and LinkedIn, from code review refs #28473
• src/hg/htdocs/images/newsArchImages/scRNAseq.png
  • lines changed 0, context: html, text, full: html, text
    7494759afb5219ac153c3ff5ec2bebd67df8e58f Tue Nov 9 10:28:59 2021 -0800
    Adding new screenshot of scRNA-seq track group to test quality of image.
• src/hg/htdocs/images/newsArchImages/scRNAseq_trackgroup.jpg
  • lines changed 0, context: html, text, full: html, text
    d1bdbad932df698180604253e2d9b79fe93707bb Tue Nov 9 08:35:22 2021 -0800
    Adding image of scRNA-seq trackgroup. refs #26964
  • lines changed 0, context: html, text, full: html, text
    dcf5d9a94ead8537fefd3ef4f70ecc956dfebc86 Tue Nov 9 10:16:11 2021 -0800
    Adding new better resolution screenshot. refs #26964
• src/hg/htdocs/images/newsArchImages/scRNAseq_trackgroup.png
  • lines changed 0, context: html, text, full: html, text
    894973582add10eb0a30ac0e114676381b2d4440 Tue Nov 9 10:21:41 2021 -0800
    Adding .png version of scRNAseq track group screen shot. refs #26964
• src/hg/hubApi/apiUtils.c
  • lines changed 1, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/inc/bigRmskUi.h
  • lines changed 29, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/inc/customTrack.h
  • lines changed 2, context: html, text, full: html, text
    f3009e2f9d911795bd1d13a0f95bbbee46309f83 Sun Nov 14 18:54:39 2021 -0800
    Adding warn-and-continue option to hgCustom. Motivation is to support https warnings but will be useful more widely. refs #28458
• src/hg/inc/hgMaf.h
  • lines changed 4, context: html, text, full: html, text
    36650b61875fa047f2c9ebc3657d1a9d10ec77e6 Fri Nov 12 14:42:17 2021 -0800
    Give developers a way to map sequence names to labels in maf display refs #28495
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/js/dbDbTaxonomy.js
  • lines changed 1, context: html, text, full: html, text
    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/lib/cart.c
  • lines changed 13, context: html, text, full: html, text
    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/hg/lib/customFactory.c
  • lines changed 19, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/lib/customTrack.c
  • lines changed 12, context: html, text, full: html, text
    f3009e2f9d911795bd1d13a0f95bbbee46309f83 Sun Nov 14 18:54:39 2021 -0800
    Adding warn-and-continue option to hgCustom. Motivation is to support https warnings but will be useful more widely. refs #28458
• src/hg/lib/hgMaf.c
  • lines changed 13, context: html, text, full: html, text
    36650b61875fa047f2c9ebc3657d1a9d10ec77e6 Fri Nov 12 14:42:17 2021 -0800
    Give developers a way to map sequence names to labels in maf display refs #28495
• src/hg/lib/hui.c
  • lines changed 26, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/lib/trackDbCustom.c
  • lines changed 3, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    15973bdabacf5ddf5dd9289d05e83a7cd4080dbb Tue Nov 9 09:12:48 2021 -0800
    support for bigRmsk from Robert Hubley robert.hubley@isbscience.org
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 99, context: html, text, full: html, text
    e303c9b8fc40e8cc55a0186148cef1d54108c126 Fri Nov 12 17:24:03 2021 -0800
    sheep GCF_002742125.1 vs. OviAri4 lastz/chain/net run for user, refs #28463
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 11, context: html, text, full: html, text
    295507e8b1564ed230de1443c145ab6af08009db Tue Nov 9 09:18:25 2021 -0800
    adding 12 new birds from VGP project no redmine
  • lines changed 2, context: html, text, full: html, text
    f163330f665d841c45b6cb918b97eb53c35bc337 Fri Nov 12 20:14:34 2021 -0800
    catching up two VGP bird assemblies no redmine
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    7a3f0ff1bec943668e0379ca2694b3c2541c29ea Tue Nov 9 09:28:13 2021 -0800
    adding 11 new birds for the VGP project no redmine
  • lines changed 2, context: html, text, full: html, text
    e662538aa03114cd10f1422293519ac6514691de Fri Nov 12 20:14:04 2021 -0800
    catching up two VGP bird assemblies no redmine
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    c11558b1ff481df5fe70896af27eeeaa15526147 Tue Nov 9 15:43:13 2021 -0800
    Removing aliases refs #28322
• src/hg/makeDb/doc/mm10.txt
  • lines changed 2, context: html, text, full: html, text
    c11558b1ff481df5fe70896af27eeeaa15526147 Tue Nov 9 15:43:13 2021 -0800
    Removing aliases refs #28322
• src/hg/makeDb/doc/myoLuc1.txt
  • lines changed 19, context: html, text, full: html, text
    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 12, context: html, text, full: html, text
    3c5559e0b9c631efa8773872e1eb45c2498c40af Thu Nov 11 21:34:26 2021 -0800
    update common name for Microbat refs #28469
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.sh
  • lines changed 10, context: html, text, full: html, text
    b5c461e5c49abf9eb5a708e2b63243555b2362da Wed Nov 10 18:05:28 2021 -0800
    first cut at a sequence logo track, also some makeDoc for gene tracks
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM28.sh
  • lines changed 10, context: html, text, full: html, text
    b5c461e5c49abf9eb5a708e2b63243555b2362da Wed Nov 10 18:05:28 2021 -0800
    first cut at a sequence logo track, also some makeDoc for gene tracks
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 1, context: html, text, full: html, text
    ee32bb6814651383d9ad925fd6adbb43c255aa22 Tue Nov 9 16:03:44 2021 -0800
    Fix buildTrix in makeDb/trackDb/ to use maxWordLength=64 so ixIxx which reports errors now is happy.
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/human/hg38/bloodHao.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/colonWang.html
  • lines changed 27, context: html, text, full: html, text
    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
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    c5a4f1220fcdf9da6f2f689cba6c5da4e894cb1e Thu Nov 4 16:02:39 2021 -0700
    Adding a sentence about updated coloring for Donor track. refs #26969
  • lines changed 5, context: html, text, full: html, text
    4d39c4b63258cfc8ace9999d820ab12b71b5a8ad Fri Nov 5 05:46:42 2021 -0700
    Added authors to credits section.
• src/hg/makeDb/trackDb/human/hg38/colonWang.ra
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    b26bf6e184e14a609298eb0f4a643dcb22edc545 Thu Nov 4 10:16:24 2021 -0700
    Adding barChartCategoryUrl setting to tracks that have updated coloring. refs #26964
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
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    40ac97854a58aaea94730af9aa7e202e01410616 Thu Nov 11 12:17:36 2021 -0800
    correct common name of two bats that were just called 'Bats'
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
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    43cb050b5f8ee625e6459f293667972df23ba2f9 Thu Nov 4 10:54:59 2021 -0700
    Fixing merge conflict.
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/ileumWang.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
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    c5a4f1220fcdf9da6f2f689cba6c5da4e894cb1e Thu Nov 4 16:02:39 2021 -0700
    Adding a sentence about updated coloring for Donor track. refs #26969
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    4d39c4b63258cfc8ace9999d820ab12b71b5a8ad Fri Nov 5 05:46:42 2021 -0700
    Added authors to credits section.
• src/hg/makeDb/trackDb/human/hg38/ileumWang.ra
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    b26bf6e184e14a609298eb0f4a643dcb22edc545 Thu Nov 4 10:16:24 2021 -0700
    Adding barChartCategoryUrl setting to tracks that have updated coloring. refs #26964
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
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    b26bf6e184e14a609298eb0f4a643dcb22edc545 Thu Nov 4 10:16:24 2021 -0700
    Adding barChartCategoryUrl setting to tracks that have updated coloring. refs #26964
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/rectumWang.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
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    c5a4f1220fcdf9da6f2f689cba6c5da4e894cb1e Thu Nov 4 16:02:39 2021 -0700
    Adding a sentence about updated coloring for Donor track. refs #26969
• src/hg/makeDb/trackDb/human/hg38/rectumWang.ra
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    b26bf6e184e14a609298eb0f4a643dcb22edc545 Thu Nov 4 10:16:24 2021 -0700
    Adding barChartCategoryUrl setting to tracks that have updated coloring. refs #26964
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.html
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    79594c5fc4325c99ddd6f7e78ab66b4a7e22ce9f Thu Nov 4 09:26:35 2021 -0700
    Moved Data Access section and made small edits based on Redmine comments from QA. refs #26964
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    b62a6e539101bbc13e8082f77064d1622835594a Thu Nov 4 10:38:21 2021 -0700
    Added a new spleenMadissoon track.
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    43cb050b5f8ee625e6459f293667972df23ba2f9 Thu Nov 4 10:54:59 2021 -0700
    Fixing merge conflict.
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    02dc7d46a50e45c5b9ce9a8f02297b56d44bd2d9 Wed Nov 10 14:19:12 2021 -0800
    Adding url override for orphanet track, refs #14319
• src/hg/makeDb/trackDb/human/jaspar.html
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    79608c6c698057d341651acf5e2cf34033240259 Wed Nov 10 13:48:57 2021 -0800
    small word-order change
• src/hg/makeDb/trackDb/human/newChainNet.ra
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/human/orphadata.html
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    b4946dbcea6eb9677cd8a09b2a8f499a0bde0b54 Wed Nov 10 14:34:32 2021 -0800
    Edits to OrphaNet track refs #14319
• src/hg/makeDb/trackDb/human/trackDb.ra
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    b4946dbcea6eb9677cd8a09b2a8f499a0bde0b54 Wed Nov 10 14:34:32 2021 -0800
    Edits to OrphaNet track refs #14319
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    deb99eff8c007089e2fc6bdc5ffc91bda293cfc7 Wed Nov 10 16:34:49 2021 -0800
    Changing release date for orphanet refs #14319
• src/hg/makeDb/trackDb/makefile
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    ee32bb6814651383d9ad925fd6adbb43c255aa22 Tue Nov 9 16:03:44 2021 -0800
    Fix buildTrix in makeDb/trackDb/ to use maxWordLength=64 so ixIxx which reports errors now is happy.
• src/hg/makeDb/trackDb/microbat/myoLuc1/description.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    bcb2ebe2ea3d2023b54ffd993b646db0bc81183c Wed Nov 10 16:53:29 2021 -0800
    Updating dataVersion for problematicSites (release alpha).
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    167a32af895517043e706a408a0ac09e14ec4763 Thu Nov 11 10:10:59 2021 -0800
    Updating problematic sites track refs #28490
• src/hg/pslStats/pslStats.c
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    e941a68c6f3089528741d24330b8ef04999a47fe Sun Nov 14 15:03:29 2021 -0800
    added option to output TSV-style header
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    1279043d2cb8d519a1ef0a7d1b80f6ab721d4b1f Sun Nov 14 15:10:36 2021 -0800
    make TSV header work on other output files
• src/hg/pslStats/tests/expected/tsvHeaderTest.stats
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    e941a68c6f3089528741d24330b8ef04999a47fe Sun Nov 14 15:03:29 2021 -0800
    added option to output TSV-style header
• src/hg/pslStats/tests/makefile
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    e941a68c6f3089528741d24330b8ef04999a47fe Sun Nov 14 15:03:29 2021 -0800
    added option to output TSV-style header
• src/hg/rnaStructure/rnaPhylo/genomes.txt
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/utils/automation/configFiles/myoLuc1.config.ra
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/utils/automation/configFiles/myoLuc2.config.ra
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/utils/hubCheck/hubCheck.c
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    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    5d2d3c7da2b3486fce37bbf4f268ea4ff85f4f91 Sun Nov 7 10:03:09 2021 -0800
    Fixing mutations for Nextstrain clades 21A (Delta) and 21H (Mu): A28461G is not required by clades.tsv and can occur later in the big tree path; 24410 is now masked & needs to be N in both Delta and Mu.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    9fb997565b120c0e299e5c421e9ed6a409d18da9 Sun Nov 7 10:08:07 2021 -0800
    Added new lineages from pango-designation releases v1.2.92 and v1.2.93. Adjusted sets of mutations (mostly adding masked bases, most of those for sites deleted in Delta but reported as mutations by some genome assembly pipelines) for existing lineages.
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    62b4b182a499b110f3bc2045b7859bc20e82e5e8 Wed Nov 10 17:03:41 2021 -0800
    Adding missing mutation C1427T to P.1.10 (also mask 11296).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    883a8a9699c47c71ab36838cc0ec878b1831cd0f Sun Nov 7 10:10:26 2021 -0800
    Nextstrain clades are now completely specified by nextstrain.clade-mutations.tsv; -c (--clade-names) input file is ignored, so no need to pass it in.
• src/hg/utils/phyloTrees/commonNames.sh
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/hg/utils/phyloTrees/placentals.txt
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    e18510fd8cce5a41aac912da2ca49fa910e2bc5f Fri Nov 12 07:35:55 2021 -0800
    updated doc for metabat common name fix
• src/inc/net.h
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    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/lib/https.c
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    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/lib/net.c
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    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/product/ex.hg.conf
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    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/product/mirrorManual.txt
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    5b281c69d7c3d44aeada5a1b0ed152d345adf2e8 Tue Nov 9 11:09:59 2021 -0800
    Squashed commit of the following: Adding new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables for CGIs that use the cart. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility. refs #28332, #28457, #28458
• src/utils/qa/weeklybld/buildEnv.csh
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    0dafeb33fc09ddfabfdf863a0ca5bc50830116b4 Mon Nov 15 10:13:47 2021 -0800
    v424 preview1, refs #28404

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