All File Changes

v433_base to v434_preview (2022-06-27 to 2022-07-05) v434

• src/hg/htdocs/FAQ/FAQdownloads.html
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    84018a1d6515b75a60de04a61dd6f3f80be38580 Tue Jul 5 09:32:02 2022 -0700
    Adding a link in hgTracksHelp.html, linked to from liftOver CGI, to a new anchor on FAQdownloads#liftOver that provides an example of running the command-line tool, refs #29698
• src/hg/htdocs/contacts.html
  • lines changed 5, context: html, text, full: html, text
    e1933904584d5aa8589b4edd6574b01492b1a8c8 Thu Jun 30 07:47:01 2022 -0700
    Updating contacts.html to use newer gbstaff21.jpg vs older gbstaff16.jpg
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    5e7ae9c0bddd97efa236e2a138e00e9ccc5dda1e Thu Jun 30 12:08:57 2022 -0700
    Adding the track hub settings blog post link to help pages, refs #28817
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 6, context: html, text, full: html, text
    7f32dedc0a1e4440d15bdeb8bcf2b2eb43abc663 Tue Jun 28 06:59:27 2022 -0700
    Adding image in hgTracksHelp.html of configuration panel, no RM
  • lines changed 31, context: html, text, full: html, text
    1b93ecbcf4117e938f8c1050ed32ef1a0876156a Wed Jun 29 06:58:58 2022 -0700
    Rearranging info. sections about configuration options to match the order they appear, and adding image display for next/previous gray/white arrows, no RM
  • lines changed 4, context: html, text, full: html, text
    5e7ae9c0bddd97efa236e2a138e00e9ccc5dda1e Thu Jun 30 12:08:57 2022 -0700
    Adding the track hub settings blog post link to help pages, refs #28817
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    10cae91dae74e7ced53a27654cc4f58bfd659dcf Sat Jul 2 12:45:08 2022 -0700
    Adding suggested change from CR refs #29655
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    84018a1d6515b75a60de04a61dd6f3f80be38580 Tue Jul 5 09:32:02 2022 -0700
    Adding a link in hgTracksHelp.html, linked to from liftOver CGI, to a new anchor on FAQdownloads#liftOver that provides an example of running the command-line tool, refs #29698
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 10, context: html, text, full: html, text
    f523ee549b4a0e3068811b8f6bf01b8f58124b8c Mon Jun 27 15:20:56 2022 -0700
    Fixing up the trackDb documentation and renaming some variables: extraDetailsTable -> detailsStaticTable, extraTableFields -> detailsDynamicTable
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 10, context: html, text, full: html, text
    f523ee549b4a0e3068811b8f6bf01b8f58124b8c Mon Jun 27 15:20:56 2022 -0700
    Fixing up the trackDb documentation and renaming some variables: extraDetailsTable -> detailsStaticTable, extraTableFields -> detailsDynamicTable
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 86, context: html, text, full: html, text
    f523ee549b4a0e3068811b8f6bf01b8f58124b8c Mon Jun 27 15:20:56 2022 -0700
    Fixing up the trackDb documentation and renaming some variables: extraDetailsTable -> detailsStaticTable, extraTableFields -> detailsDynamicTable
  • lines changed 1, context: html, text, full: html, text
    0672042b30809ee5f4365995ff643e063f4d3ebf Tue Jun 28 09:22:35 2022 -0700
    Fixing typo in maxWindowCoverage description, refs #28817
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 25, context: html, text, full: html, text
    aa807eaeadff6c4f4d3c19a2783a5677d4f3801f Thu Jun 30 14:17:24 2022 -0700
    Updating news for the hg38 gnomadPLI track, refs #29358
• src/hg/htdocs/images/configureMenu.png
  • lines changed 0, context: html, text, full: html, text
    2149d6c178a51972053b5242bd9eb4619dcbb3c2 Tue Jun 28 06:52:09 2022 -0700
    Adding a picture of configuration page
• src/hg/htdocs/images/gbstaff21.jpg
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    7433a54efa964ca85c7e4ef414a8405545c9b71d Thu Jun 30 07:45:55 2022 -0700
    Adding an updated staff image to replace gbstaff16.jpg
• src/hg/htdocs/images/nextItem.png
  • lines changed 0, context: html, text, full: html, text
    3198de8779b6d02342e529972ba4966de2d2a0e7 Wed Jun 29 06:56:40 2022 -0700
    Adding an image for gray/white arrows of next/previous items.
• src/hg/htdocs/images/snowflake.png
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    bc1d5b8d6a0065139e16d32d527e06078e5c3512 Thu Jun 30 15:09:56 2022 -0700
    Adding snowflake to indicate data freeze, refs #29694
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    aa807eaeadff6c4f4d3c19a2783a5677d4f3801f Thu Jun 30 14:17:24 2022 -0700
    Updating news for the hg38 gnomadPLI track, refs #29358
• src/hg/htdocs/staff.html
  • lines changed 8, context: html, text, full: html, text
    d2960194d39bc49f8ec9f6aa6d61bc74efa20f8e Fri Jul 1 10:54:50 2022 -0700
    Adding Max's new position to staff page in response to grant state July 1st, no RM.
• src/hg/js/hgHubConnect.js
  • lines changed 9, context: html, text, full: html, text
    f9a3c489186a9c3bedd1548ea86394964769062c Thu Jun 30 02:16:26 2022 -0700
    fixing copy button which mysteriously broke after build, refs #29583
  • lines changed 4, context: html, text, full: html, text
    5edf4ac72866f696753442f60b6ab1e3c984f381 Tue Jul 5 05:03:30 2022 -0700
    remove tag order dependency in javascript code, refs #29696, remove alert text URL, refs #29583. Hopefully the last suggestions for a tiny feature.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 23, context: html, text, full: html, text
    e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 Wed Jun 29 18:44:29 2022 -0700
    Creating metaDome track, refs #23883
  • lines changed 5, context: html, text, full: html, text
    c67f70fced286da481cf4a3c73013d1d2fca909b Fri Jul 1 07:07:13 2022 -0700
    adding lrg ncbi accession to search specs, refs #29689
  • lines changed 18, context: html, text, full: html, text
    5000aa2e1caad21d2066d15d087deb95945b17db Fri Jul 1 09:12:41 2022 -0700
    adding missing makedoc for special regions track on hg19, refs #29685
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 6, context: html, text, full: html, text
    c67f70fced286da481cf4a3c73013d1d2fca909b Fri Jul 1 07:07:13 2022 -0700
    adding lrg ncbi accession to search specs, refs #29689
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    5dfc4d7bea7e5af7d5e72cfbb65bdafd82de1eda Wed Jun 29 11:10:35 2022 -0700
    fixed up the large genomes for grasshopper and locust refs #29545
• src/hg/makeDb/scripts/metaDome/buildMetaDomeTracks.py
  • lines changed 107, context: html, text, full: html, text
    e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 Wed Jun 29 18:44:29 2022 -0700
    Creating metaDome track, refs #23883
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 29, context: html, text, full: html, text
    d7a5dfe14d2495eed1b79a0171768bf6822193b3 Mon Jun 27 12:06:48 2022 -0700
    Adding Data Access section to track description page, refs #29153
  • lines changed 64, context: html, text, full: html, text
    e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 Wed Jun 29 18:44:29 2022 -0700
    Creating metaDome track, refs #23883
• src/hg/makeDb/trackDb/human/constraintSuper.ra
  • lines changed 2, context: html, text, full: html, text
    e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 Wed Jun 29 18:44:29 2022 -0700
    Creating metaDome track, refs #23883
• src/hg/makeDb/trackDb/human/hg19/problematic-public.ra
  • lines changed 117, context: html, text, full: html, text
    37a057e31b8bb89bb901bbbc17cc4b21dd0a632c Wed Jun 29 07:05:34 2022 -0700
    making problematic regions / manual comments searchable, refs #29685
• src/hg/makeDb/trackDb/human/hg19/problematic.html
  • lines changed 5, context: html, text, full: html, text
    37a057e31b8bb89bb901bbbc17cc4b21dd0a632c Wed Jun 29 07:05:34 2022 -0700
    making problematic regions / manual comments searchable, refs #29685
• src/hg/makeDb/trackDb/human/hg19/problematic.ra
  • lines changed 125, context: html, text, full: html, text
    37a057e31b8bb89bb901bbbc17cc4b21dd0a632c Wed Jun 29 07:05:34 2022 -0700
    making problematic regions / manual comments searchable, refs #29685
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 129, context: html, text, full: html, text
    37a057e31b8bb89bb901bbbc17cc4b21dd0a632c Wed Jun 29 07:05:34 2022 -0700
    making problematic regions / manual comments searchable, refs #29685
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 4, context: html, text, full: html, text
    c03d749ab8f078147ddfc671998f4abfbce0bf18 Mon Jun 27 12:22:05 2022 -0700
    Updating shortLabel’s and the download server link, refs #29358
  • lines changed 2, context: html, text, full: html, text
    f523ee549b4a0e3068811b8f6bf01b8f58124b8c Mon Jun 27 15:20:56 2022 -0700
    Fixing up the trackDb documentation and renaming some variables: extraDetailsTable -> detailsStaticTable, extraTableFields -> detailsDynamicTable
  • lines changed 2, context: html, text, full: html, text
    abb761724cf2eb07e31e9a9cbed614ba276e9e7f Tue Jun 28 17:31:43 2022 -0700
    Removing itemRgb on line, from missenseByGene and missenseByTranscript stanza, refs #29358
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    19f07669f87b28e20492d005cf692b37edaeb61a Wed Jun 29 15:45:55 2022 -0700
    Updating pennantIcons for the hg38 gnomadPLI track, refs #29358
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    c03d749ab8f078147ddfc671998f4abfbce0bf18 Mon Jun 27 12:22:05 2022 -0700
    Updating shortLabel’s and the download server link, refs #29358
• src/hg/makeDb/trackDb/human/metaDome.ra
  • lines changed 27, context: html, text, full: html, text
    e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 Wed Jun 29 18:44:29 2022 -0700
    Creating metaDome track, refs #23883
• src/hg/makeDb/trackDb/human/mtr.ra
  • lines changed 1, context: html, text, full: html, text
    e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 Wed Jun 29 18:44:29 2022 -0700
    Creating metaDome track, refs #23883
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    c67f70fced286da481cf4a3c73013d1d2fca909b Fri Jul 1 07:07:13 2022 -0700
    adding lrg ncbi accession to search specs, refs #29689
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5fec215faa9752a1c44260dec8f8932455ed0ebf Fri Jul 1 07:08:46 2022 -0700
    fixing varskip track and also making resistance mutations a default track, refs #28889
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    a1571d1c5f3bef283dd9291f783202a576b3581f Fri Jul 1 13:30:33 2022 -0700
    Removing B117 in USA track and releasing update for resist track refs #28889
• src/hg/makeDb/trackDb/virus/wuhCor1/varskip.ra
  • lines changed 15, context: html, text, full: html, text
    5fec215faa9752a1c44260dec8f8932455ed0ebf Fri Jul 1 07:08:46 2022 -0700
    fixing varskip track and also making resistance mutations a default track, refs #28889
• src/hg/ratStuff/mafCounts/mafCounts.c
  • lines changed 1, context: html, text, full: html, text
    1ed3d40ffbe5dbf9059f99e71b757f26d136fe8f Fri Jul 1 14:44:05 2022 -0700
    make usage message a bit more clear.
• src/hg/utils/otto/lrg/buildLrg.sh
  • lines changed 1, context: html, text, full: html, text
    c67f70fced286da481cf4a3c73013d1d2fca909b Fri Jul 1 07:07:13 2022 -0700
    adding lrg ncbi accession to search specs, refs #29689
• src/hg/utils/otto/lrg/checkLrg.sh
  • lines changed 1, context: html, text, full: html, text
    c67f70fced286da481cf4a3c73013d1d2fca909b Fri Jul 1 07:07:13 2022 -0700
    adding lrg ncbi accession to search specs, refs #29689
• src/lib/https.c
  • lines changed 10, context: html, text, full: html, text
    504de1431be915e85967969706a41d9e23b962b6 Wed Jun 29 15:34:25 2022 -0700
    We need to call openSslInit() first before using all other variables, including https_proxy. Easily fixed. This was reported by a user Volker Weinberger on the mailing list.
• src/utils/qa/weeklybld/buildEnv.csh
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    e550cffc50cadc1672e4398f462bfb11c9b59623 Tue Jul 5 10:05:41 2022 -0700
    v434 preview1, refs #29585

• lines changed: 940
• files changed: 50