All File Changes

v439_preview to v439_preview2 (2022-10-17 to 2022-10-24) v439

• src/hg/hgSearch/hgSearch.c
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    bfc66e321227aee4b768698682efc18733ce3ff8 Thu Oct 20 16:16:01 2022 -0700
    Include footer at the bottom of the search page, refs #29693
  • lines changed 13, context: html, text, full: html, text
    fccc494337013c07d32c506fec1ae07a5b93ff88 Sun Oct 23 17:00:03 2022 -0700
    deal with curated assemblies in hgSearch
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
• src/hg/hgTracks/wigCommon.h
  • lines changed 1, context: html, text, full: html, text
    3b0398668f40703ec7342f657267c312a011a2bb Wed Oct 19 13:09:55 2022 -0700
    add sum mode to the possible windowing methods for wiggles.
• src/hg/hgTracks/wigTrack.c
  • lines changed 3, context: html, text, full: html, text
    3b0398668f40703ec7342f657267c312a011a2bb Wed Oct 19 13:09:55 2022 -0700
    add sum mode to the possible windowing methods for wiggles.
  • lines changed 1, context: html, text, full: html, text
    ab64e884e099ac67de02d4b23e87dbe2d72eebd9 Wed Oct 19 15:41:57 2022 -0700
    mouseovers for wiggles show the value being graphed, not (necessarily) the mean.
• src/hg/htdocs/style/mouseOver.css
  • lines changed 1, context: html, text, full: html, text
    1313ab4f97f5d5c1f2edd63533dce23ad8426ab7 Wed Oct 19 10:50:11 2022 -0700
    draw zoom indicator box in the right place and make it transparent so you can see the underlying pixel
• src/hg/inc/hubConnect.h
  • lines changed 2, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    3b0398668f40703ec7342f657267c312a011a2bb Wed Oct 19 13:09:55 2022 -0700
    add sum mode to the possible windowing methods for wiggles.
• src/hg/js/hgGateway.js
  • lines changed 10, context: html, text, full: html, text
    fccc494337013c07d32c506fec1ae07a5b93ff88 Sun Oct 23 17:00:03 2022 -0700
    deal with curated assemblies in hgSearch
• src/hg/js/hgSearch.js
  • lines changed 6, context: html, text, full: html, text
    2dbbdd8d731791ab5ba3354b1b5bb41e82d99c84 Wed Oct 19 10:05:23 2022 -0700
    Fix search client to indicate when there are no results, refs #29693
  • lines changed 2, context: html, text, full: html, text
    f5ce127821bae4c11e81c2491d789af5a443f076 Thu Oct 20 15:43:58 2022 -0700
    Add space after button, refs #29693
  • lines changed 14, context: html, text, full: html, text
    fccc494337013c07d32c506fec1ae07a5b93ff88 Sun Oct 23 17:00:03 2022 -0700
    deal with curated assemblies in hgSearch
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    1313ab4f97f5d5c1f2edd63533dce23ad8426ab7 Wed Oct 19 10:50:11 2022 -0700
    draw zoom indicator box in the right place and make it transparent so you can see the underlying pixel
  • lines changed 4, context: html, text, full: html, text
    ab64e884e099ac67de02d4b23e87dbe2d72eebd9 Wed Oct 19 15:41:57 2022 -0700
    mouseovers for wiggles show the value being graphed, not (necessarily) the mean.
• src/hg/js/utils.js
  • lines changed 11, context: html, text, full: html, text
    fccc494337013c07d32c506fec1ae07a5b93ff88 Sun Oct 23 17:00:03 2022 -0700
    deal with curated assemblies in hgSearch
• src/hg/lib/bigBedFind.c
  • lines changed 2, context: html, text, full: html, text
    749fbba847b9900a488e1ae88dc46c3d7fbedc15 Fri Oct 21 15:55:28 2022 -0700
    Fix wrong short circuit check in determining whether a bigBed has a search index or not, refs #30156
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
• src/hg/lib/hubConnect.c
  • lines changed 19, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    3b0398668f40703ec7342f657267c312a011a2bb Wed Oct 19 13:09:55 2022 -0700
    add sum mode to the possible windowing methods for wiggles.
• src/hg/lib/web.c
  • lines changed 4, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 21, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 46, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 50, context: html, text, full: html, text
    f929af1c968f978096b4be711d0f7b375fa73ce1 Mon Oct 17 17:19:11 2022 -0700
    recent update moved 18 into legacy refs #29545
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    195b248812ca983e403a54b455a2a11e92835e10 Mon Oct 17 20:27:26 2022 -0700
    clean up this list for recent updates refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 22, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    895d6005e6603d29b67c3166b5544b442a615d5d Mon Oct 17 16:34:09 2022 -0700
    adding 85 assemblies update refs #29545
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg19/gnomadCoverage.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg19/gnomadExomesGenomes.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg19/gnomadPext.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg19/gnomadSv.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg19/gnomadVariants.html
  • lines changed 1, context: html, text, full: html, text
    761811f2dcf88f37f6cb21f456f5fe961af854df Thu Oct 20 14:39:33 2022 -0700
    Fixing typo on description page for hg19 gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    118f115d7a6d3280c96084390760e9db5f31f5d5 Wed Oct 19 08:02:42 2022 -0700
    tiny change to gnomad mutation score requested by authors, no redmine
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    7bf56823977346d80012ad28896f3e18e4cd6fbd Wed Oct 19 08:08:52 2022 -0700
    add a note about the gnomad mutation update, refs #30160
  • lines changed 1, context: html, text, full: html, text
    67a1cdb12c8562296beb118f3e04cba747422483 Thu Oct 20 13:43:24 2022 -0700
    Fixing typo on description page for gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    67a1cdb12c8562296beb118f3e04cba747422483 Thu Oct 20 13:43:24 2022 -0700
    Fixing typo on description page for gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1.html
  • lines changed 1, context: html, text, full: html, text
    67a1cdb12c8562296beb118f3e04cba747422483 Thu Oct 20 13:43:24 2022 -0700
    Fixing typo on description page for gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 1, context: html, text, full: html, text
    67a1cdb12c8562296beb118f3e04cba747422483 Thu Oct 20 13:43:24 2022 -0700
    Fixing typo on description page for gnomAD tracks, refs #30175
• src/hg/makeDb/trackDb/human/hgnc.html
  • lines changed 13, context: html, text, full: html, text
    bbd718a03c8042b1ff26617d7dd2964463e745f4 Fri Oct 21 10:43:48 2022 -0700
    Final tdb changes for hgnc and panelapp refs #30097, #29891
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 1, context: html, text, full: html, text
    bbd718a03c8042b1ff26617d7dd2964463e745f4 Fri Oct 21 10:43:48 2022 -0700
    Final tdb changes for hgnc and panelapp refs #30097, #29891
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    bbd718a03c8042b1ff26617d7dd2964463e745f4 Fri Oct 21 10:43:48 2022 -0700
    Final tdb changes for hgnc and panelapp refs #30097, #29891
• src/hg/makeDb/trackDb/virus/wuhCor1/recomb.html
  • lines changed 5, context: html, text, full: html, text
    233692eb3a00e65fffd3d4fc0c4dbf4e10d86d6a Mon Oct 17 17:31:29 2022 -0700
    Changes for double quotes with the HTML from code review, refs #30152
• src/hg/utils/otto/clinvar/clinvarSubLolly
  • lines changed 20, context: html, text, full: html, text
    1313ab4f97f5d5c1f2edd63533dce23ad8426ab7 Wed Oct 19 10:50:11 2022 -0700
    draw zoom indicator box in the right place and make it transparent so you can see the underlying pixel
• src/hg/utils/otto/otto.crontab
  • lines changed 16, context: html, text, full: html, text
    c007c45aa910f36c35e0e774e02a7dd63a2264bf Mon Oct 17 03:14:56 2022 -0700
    bringing git otto crontab in sync with reality, no redmine
  • lines changed 3, context: html, text, full: html, text
    13d39740c6886cea8c182e53a7cff5afe9fc2048 Thu Oct 20 13:15:53 2022 -0700
    Adding the panelApp otto link refs #25568
  • lines changed 7, context: html, text, full: html, text
    57ffdcc953a23b7f60b084b1cb3c9706f0460303 Fri Oct 21 02:09:19 2022 -0700
    updating crontab, adding panelApp otto job, refs #25568
• src/inc/cheapcgi.h
  • lines changed 3, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
  • lines changed 3, context: html, text, full: html, text
    342e188223ed7869383cf696984501d38a0ff0d1 Fri Oct 21 02:04:47 2022 -0700
    adding a more generic way to add javascript events to DOM elements, no redmine
• src/lib/cheapcgi.c
  • lines changed 17, context: html, text, full: html, text
    97b899f21a0804a3f9e025fca3e1a785db9cb6fe Wed Oct 19 17:18:31 2022 -0700
    get the clade, org, and db dropdowns in hgTables to work with curated hubs
  • lines changed 8, context: html, text, full: html, text
    342e188223ed7869383cf696984501d38a0ff0d1 Fri Oct 21 02:04:47 2022 -0700
    adding a more generic way to add javascript events to DOM elements, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    6a15131015d6c1bc701cfc99d5bb36cc892b678a Mon Oct 24 10:06:42 2022 -0700
    v439 preview2, refs #30145

• lines changed: 738
• files changed: 59