All File Changes

v464_base to v465_preview (2024-04-22 to 2024-04-29) v465

• docs/gb101.md
  • lines changed 166, context: html, text, full: html, text
    a8d8d0e805bc550786aef8570670c5d16ffb65ee Sun Apr 28 18:32:11 2024 -0700
    updated index, added gb101.md stub, added page_template.md refs #30335
• docs/index.md
  • lines changed 69, context: html, text, full: html, text
    a8d8d0e805bc550786aef8570670c5d16ffb65ee Sun Apr 28 18:32:11 2024 -0700
    updated index, added gb101.md stub, added page_template.md refs #30335
• docs/makefile
  • lines changed 4, context: html, text, full: html, text
    a8d8d0e805bc550786aef8570670c5d16ffb65ee Sun Apr 28 18:32:11 2024 -0700
    updated index, added gb101.md stub, added page_template.md refs #30335
• docs/markdown_template.md
  • lines changed 40, context: html, text, full: html, text
    a8d8d0e805bc550786aef8570670c5d16ffb65ee Sun Apr 28 18:32:11 2024 -0700
    updated index, added gb101.md stub, added page_template.md refs #30335
• docs/page_template.md
  • lines changed 202, context: html, text, full: html, text
    a8d8d0e805bc550786aef8570670c5d16ffb65ee Sun Apr 28 18:32:11 2024 -0700
    updated index, added gb101.md stub, added page_template.md refs #30335
• src/hg/hgBlat/hgBlat.c
  • lines changed 20, context: html, text, full: html, text
    dd8801fc68f0f93f889aa15436b63dbbfc13aa04 Mon Apr 22 17:06:03 2024 -0700
    add 'in new tab' link to hgBlat output, user asked me after seven years at my poster why we never fixed this. What a life. refs #19668
  • lines changed 9, context: html, text, full: html, text
    d3a6ae3671e186b98e76f41f4fbf4e70190c2272 Tue Apr 23 07:23:38 2024 -0700
    adding an info icon to the create custom tracks hgBlat button, no redmine
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 115, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
• src/hg/hgTracks/encode.c
  • lines changed 4, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    4c4ae598f12f60f9281cb81b34f81d802beb0744 Mon Apr 22 11:25:53 2024 -0700
    it turns out that initTrackList() gets called twice if a nextItem arrow is pressed. Probably there are other bugs because of this, but this fixes one of them.
  • lines changed 14, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
  • lines changed 1, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    759dffc454d77d37bd807691f91a30871b315051 Mon Apr 22 17:13:10 2024 -0700
    changing exon text, refs #33506
  • lines changed 1, context: html, text, full: html, text
    d0c3cbdc054376c6654f0a401b1c31baea5a8713 Thu Apr 25 15:28:28 2024 -0700
    fix assert error
• src/hg/hgc/bamClick.c
  • lines changed 5, context: html, text, full: html, text
    bc9f54cc38a4f72f3a53c3e7bedccec41a1870be Mon Apr 29 06:26:58 2024 -0700
    adding space and skipping long cigar strings on hgc page, refs #33292
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 28, context: html, text, full: html, text
    f89a906b46c4848dee65ca534ad0962531dbb2e6 Thu Apr 25 00:12:09 2024 -0700
    Fix for hgcentralTidy cleaner, handle unsigned int ID over 2 billion correctly. This will work until we someday exceed the 4 billion sessions which make the maximum the field can take. I did not want to work, but the failures were too important to ignore. If the tables are not cleaned regularly, they grow very fast indeed. I have manually run the purge to catch up. We should be good now.
  • lines changed 1, context: html, text, full: html, text
    d7e95660922d37a73fcffc7df18bcc37af5fc458 Sat Apr 27 18:47:40 2024 -0700
    Tweak mysql data size for squeal.
• src/hg/htdocs/contacts.html
  • lines changed 404, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 105, context: html, text, full: html, text
    282b91947ea2706a4a038308a147f4783c7d1147 Mon Apr 29 01:00:41 2024 -0700
    Updating the decorator help page and adding another example on building a decorator bigBed, refs #32818
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    26becc145e422e03b2b441380aec31c1fa30e564 Tue Apr 23 17:04:50 2024 -0700
    Removing the hgHubConnect.remakeTrackHub=on setting from the hgTrackHubHelp page since it is an internal flag, refs #2110
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 33, context: html, text, full: html, text
    d808212d2c3b26fcfdd74e0720f9657b13dca67d Thu Apr 25 13:26:58 2024 -0700
    Announcing the release of the AbSplice Prediction Scores for hg19, refs #33251
  • lines changed 1, context: html, text, full: html, text
    372b3afd7324fcea69ddc0af724f4cd50ddeb6ae Thu Apr 25 17:00:02 2024 -0700
    Fixing paragraph indentation, refs #33251
  • lines changed 2, context: html, text, full: html, text
    9f3c0f2231367957a8a46854ddd444909b6b7fbd Thu Apr 25 17:06:46 2024 -0700
    Another fix to the paragraph indentation, refs #33251
• src/hg/htdocs/images/googleGroupsIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/images/hiddenIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/images/invisibleIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/images/megaphoneIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/images/trainingIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/images/twitterIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/images/youtubeIcon.png
  • lines changed 0, context: html, text, full: html, text
    04891f09dcd918aad2dced9476463b384f1e9f36 Mon Apr 22 15:55:23 2024 -0700
    Redoing the contact.html page to slim it down and improve its function. Be more clear about ML options, remove seldomly used options/lists, etc. refs #33487
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    d808212d2c3b26fcfdd74e0720f9657b13dca67d Thu Apr 25 13:26:58 2024 -0700
    Announcing the release of the AbSplice Prediction Scores for hg19, refs #33251
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
  • lines changed 1, context: html, text, full: html, text
    f4326f8ac18dde6d6da51a49327f86a9e04c948e Thu Apr 25 11:09:01 2024 -0700
    Changing the hgTracks group label color back to the original blue color, refs #33039
• src/hg/inc/bigBedFilter.h
  • lines changed 54, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    4c4ae598f12f60f9281cb81b34f81d802beb0744 Mon Apr 22 11:25:53 2024 -0700
    it turns out that initTrackList() gets called twice if a nextItem arrow is pressed. Probably there are other bugs because of this, but this fixes one of them.
  • lines changed 1, context: html, text, full: html, text
    72cb9e17cc0c0726b7bd856167daa3894ab8a115 Mon Apr 22 11:30:50 2024 -0700
    bad type definition
  • lines changed 6, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
• src/hg/js/hgTracks.js
  • lines changed 27, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/js/hui.js
  • lines changed 89, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
  • lines changed 2, context: html, text, full: html, text
    d833738fcd5c2f1eebc0d4242eeb87ac76f71005 Mon Apr 29 09:30:46 2024 -0700
    Fix bug found by Hiram when drag selecting to zoom or highlight, refs Hiram email
• src/hg/js/utils.js
  • lines changed 6, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/lib/hubConnect.c
  • lines changed 60, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
  • lines changed 5, context: html, text, full: html, text
    5647db5dc3c4c2068c5b2d349680acab2e44b6b1 Wed Apr 24 09:51:55 2024 -0700
    don't add "Hub:" before quickLift groups
• src/hg/lib/hui.c
  • lines changed 118, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/hg/lib/trackHub.c
  • lines changed 6, context: html, text, full: html, text
    4c4ae598f12f60f9281cb81b34f81d802beb0744 Mon Apr 22 11:25:53 2024 -0700
    it turns out that initTrackList() gets called twice if a nextItem arrow is pressed. Probably there are other bugs because of this, but this fixes one of them.
  • lines changed 1, context: html, text, full: html, text
    c6284d8b84b6af2a0d522ea07f8c7ca67586aa1e Mon Apr 22 13:10:42 2024 -0700
    Ooops... fixed something without testing it much
  • lines changed 47, context: html, text, full: html, text
    d1bc57639309864bb2665bd46eddfe75863f76e4 Tue Apr 23 16:42:54 2024 -0700
    rearrange how we're doing hub groups.
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 3, context: html, text, full: html, text
    d8db31ce919ec130b1f732ea979e1ea093b8af5d Mon Apr 22 15:13:49 2024 -0700
    manage flies common name correctly no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    a9bc761945fe9b9ce585dcf67f1233377e49c669 Mon Apr 22 14:19:01 2024 -0700
    adding GCA_026230145.1_icDioElon1.1 Diorhabda_elongata and GCA_008042735.1_UCB_Dleo_1.0 per users requests, refs #29545
  • lines changed 1, context: html, text, full: html, text
    7fc5d8aed70f1a512a512495ac49d936ccb9a5ac Tue Apr 23 09:55:48 2024 -0700
    adding RefSeq GRCr8 aka rn8 per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    5f09ff11f72ae29812f5cef198628ba3f28919e1 Thu Apr 25 13:16:08 2024 -0700
    adding GCA_029229535.1_icDioCarn1.1 invertebrate Diorhabda_carinata per user request, refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    ccc5f339ae0376f56707890a96a124d154810d92 Mon Apr 22 15:56:32 2024 -0700
    adding both fly D.leontia (RGN 210-13 2019) and Mediterranean tamarisk beetle (Crete 2022) per users requests, refs #29545
  • lines changed 1, context: html, text, full: html, text
    8100e665c111a0e189662b836533240eb3c2d4eb Thu Apr 25 13:22:36 2024 -0700
    adding Diorhabda_carinata larger tamarisk beetle (Uzbek primary hap 2023), refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    ac32d61468e240ce0c6d5f29eb2a33947e52075a Tue Apr 23 12:10:15 2024 -0700
    do not need the GRCr8 here any more no redmine
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    7fc5d8aed70f1a512a512495ac49d936ccb9a5ac Tue Apr 23 09:55:48 2024 -0700
    adding RefSeq GRCr8 aka rn8 per user request refs #29545
• src/hg/makeDb/outside/abSplice/AbSplice.hg38.makedoc
  • lines changed 178, context: html, text, full: html, text
    81f3ad54eaf0bc9457b2ff9d46dfe332aeaa656c Tue Apr 23 13:19:40 2024 -0700
    Adding the custom Python script for the hg38 abSplice track, refs #33251
  • lines changed 178, context: html, text, full: html, text
    0ad4891c56a2f30e1acd63dd515edc36049252fc Tue Apr 23 14:13:58 2024 -0700
    Revert "Adding the custom Python script for the hg38 abSplice track, refs #33251" This reverts commit 81f3ad54eaf0bc9457b2ff9d46dfe332aeaa656c.
  • lines changed 178, context: html, text, full: html, text
    6c803bc1056a20e242382c3481edcbba7fbd624b Tue Apr 23 17:45:35 2024 -0700
    Adding makedoc that contains the Python script for the hg38 abSplice track, refs #33251
• src/hg/makeDb/trackDb/human/abSplice.html
  • lines changed 75, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/human/abSplice.ra
  • lines changed 17, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/human/hg19/abSplice.html
  • lines changed 76, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/human/hg19/abSplice.ra
  • lines changed 16, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/human/hg19/knownGeneV45lift37.html
  • lines changed 178, context: html, text, full: html, text
    4b3dd9e844b2a6c502e5405e70f7976e30df7225 Thu Apr 25 13:13:51 2024 -0700
    knownGeneV45lift37 on hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 31, context: html, text, full: html, text
    a6aaa3139f34f741d82d14c803bedef875620530 Tue Apr 23 11:05:31 2024 -0700
    Removing hg19 gnomadExomesTest track that was used for QA testing, refs #32916
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/human/hg38/abSplice.html
  • lines changed 77, context: html, text, full: html, text
    81f3ad54eaf0bc9457b2ff9d46dfe332aeaa656c Tue Apr 23 13:19:40 2024 -0700
    Adding the custom Python script for the hg38 abSplice track, refs #33251
  • lines changed 77, context: html, text, full: html, text
    0ad4891c56a2f30e1acd63dd515edc36049252fc Tue Apr 23 14:13:58 2024 -0700
    Revert "Adding the custom Python script for the hg38 abSplice track, refs #33251" This reverts commit 81f3ad54eaf0bc9457b2ff9d46dfe332aeaa656c.
• src/hg/makeDb/trackDb/human/hg38/abSplice.ra
  • lines changed 16, context: html, text, full: html, text
    81f3ad54eaf0bc9457b2ff9d46dfe332aeaa656c Tue Apr 23 13:19:40 2024 -0700
    Adding the custom Python script for the hg38 abSplice track, refs #33251
  • lines changed 16, context: html, text, full: html, text
    0ad4891c56a2f30e1acd63dd515edc36049252fc Tue Apr 23 14:13:58 2024 -0700
    Revert "Adding the custom Python script for the hg38 abSplice track, refs #33251" This reverts commit 81f3ad54eaf0bc9457b2ff9d46dfe332aeaa656c.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 36, context: html, text, full: html, text
    a21526733fec1b6e7930fae4758e1688aa125383 Tue Apr 23 10:30:40 2024 -0700
    Removing test gnomad v3.1.1 track that was for QA testing only
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    d4262bca1e7f48775cd45562ff7e8a77dae739b1 Wed Apr 24 11:41:11 2024 -0700
    Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
  • lines changed 879, context: html, text, full: html, text
    464078525816d376c389e73c283e0ee40b6d0f2b Mon Apr 22 21:36:46 2024 -0700
    add a number of T2T primates no redmine
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 2, context: html, text, full: html, text
    5cd7aa7b3364cb744c638c16fd0ca95015dd6079 Thu Apr 25 09:57:53 2024 -0700
    small change to allow script to recognize knownGeneV<number><anyText> as a mammal.
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 16, context: html, text, full: html, text
    733ba7b804e84d7b60ccad1f137398ecd52db983 Tue Apr 23 18:15:09 2024 -0700
    Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507
• src/lib/bamFile.c
  • lines changed 1, context: html, text, full: html, text
    bc9f54cc38a4f72f3a53c3e7bedccec41a1870be Mon Apr 29 06:26:58 2024 -0700
    adding space and skipping long cigar strings on hgc page, refs #33292
• src/lib/htmshell.c
  • lines changed 15, context: html, text, full: html, text
    e0d9ec4b45b45a909e219e29d74fa8be55618078 Fri Apr 26 03:10:32 2024 -0700
    CSP for china tracking, refs #32535
• src/utils/qa/weeklybld/buildEnv.csh
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    e159ae03920bf96abd95109bb109dc1d026ba0c3 Mon Apr 29 10:52:15 2024 -0700
    v465 preview1, refs #33450

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• files changed: 82