All File Changes

v465_preview2 to v465_base (2024-05-06 to 2024-05-13) v465

• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    fcf958bebc396bd7aac5885e27c554087d406d7f Tue May 7 09:55:13 2024 -0700
    Sort genark searches by taxId, refs #33572
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 6, context: html, text, full: html, text
    70fc328236e32b391c3fa3cc88fb92fcb91ffa6a Tue May 7 14:17:48 2024 -0700
    Fixing Malacards link and removing the hprd link since the website is not working, refs #33080
• src/hg/hgGene/malaCards.c
  • lines changed 1, context: html, text, full: html, text
    70fc328236e32b391c3fa3cc88fb92fcb91ffa6a Tue May 7 14:17:48 2024 -0700
    Fixing Malacards link and removing the hprd link since the website is not working, refs #33080
• src/hg/hgTables/galaxy.c
  • lines changed 7, context: html, text, full: html, text
    c9cb558b37ad87c86ca3a0f1efb1a75c1b83465c Tue May 7 11:08:19 2024 -0700
    strip off hub_#_ for genark hubs when sending to Galaxy
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    651e4b46d7060ede4d9a977a1cd838f55e3315e9 Tue May 7 11:35:30 2024 -0700
    don't draw chevrons in squish mode even if intronGap is set.
• src/hg/htdocs/favicon.ico
  • lines changed 0, context: html, text, full: html, text
    9c4d89f3973972bc2e834f58df953bab5dd2c61c Sun May 12 09:44:21 2024 -0700
    Removin the favico so that we can have unique icons on dev/beta.
• src/hg/htdocs/goldenPath/help/customTrack.html
  • lines changed 22, context: html, text, full: html, text
    d88300025cbc54935141d132c49336b8d7768ac7 Mon May 6 16:09:04 2024 -0700
    Adding a table of contents to the Custom Track help page. Moving all examples to the bottom of the page. Adding summarys to some steps. Reorganizing text to be in a more digestable manor. Fixing broken links to the file formats page. Making all titles sentence case, refs #19736
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 596, context: html, text, full: html, text
    d88300025cbc54935141d132c49336b8d7768ac7 Mon May 6 16:09:04 2024 -0700
    Adding a table of contents to the Custom Track help page. Moving all examples to the bottom of the page. Adding summarys to some steps. Reorganizing text to be in a more digestable manor. Fixing broken links to the file formats page. Making all titles sentence case, refs #19736
  • lines changed 1, context: html, text, full: html, text
    fb6d02c2d2ccc402b52e78e8ca0f245de178b149 Mon May 6 16:39:51 2024 -0700
    Fixing a typo. Should be quotes not an ampersand, refs #19736
• src/hg/htdocs/indexMeetings.html
  • lines changed 10, context: html, text, full: html, text
    953766a87c0d8f7736ad95825e58fd977dd9d83e Sun May 12 09:18:36 2024 -0700
    Removing two meetings that have passed, no RM
• src/hg/htdocs/redmineWidget.html
  • lines changed 1, context: html, text, full: html, text
    a2d7bc2845a1f11846a58f49e4ada540dc8ad214 Thu May 9 09:57:33 2024 -0700
    Adding hgwalpha (another name for preview) that the security scan uses, this way we won't get RM widget spam.
• src/hg/htdocs/robots.rr.txt
  • lines changed 1, context: html, text, full: html, text
    053fb51403a3f93121f2c987189cdc28c6700bc3 Mon May 13 04:18:16 2024 -0700
    Increasing bot delay, no RM
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    3ce896cb9804962a98a273c59ce6e3ab428253b6 Sun May 12 09:12:46 2024 -0700
    making track table a tiny bit wider, Lou had the idea when sitting next to me, so no redmine
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5a48c29d628d7e98d2166bf612c2301b247d9189 Mon May 13 10:35:54 2024 -0700
    New version number v465
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    960f3316822cfedb14efb0bca174788672d9d304 Tue May 7 09:02:06 2024 -0700
    Make genoem autocomplete selections work after category label change, refs #33572
• src/hg/lib/chainArrange.as
  • lines changed 1, context: html, text, full: html, text
    675293a87172d440c9c78b1c1bdc54610bc35a77 Tue May 7 14:14:26 2024 -0700
    changes to HPRC rearrangements track in response to SAB refs #33484
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    80c38beda8680b03b5da46a287b8148ad696de40 Mon May 13 04:17:50 2024 -0700
    proving to Hiram that his life can be made easier, hiram email to browser-dev, no redmine
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    a94ab9b578fa7ff2bad82cefb1742985c55b6a76 Thu May 9 15:03:10 2024 -0700
    ongoing work on pair browser
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 3, context: html, text, full: html, text
    3a53d8fc8ac71f054e07b33173831663e1145fde Wed May 8 19:11:12 2024 -0700
    adding a couple of Apodemu per user request
  • lines changed 1, context: html, text, full: html, text
    30d3d908a1cde40a5cdee48cb033474aae735fea Fri May 10 15:51:05 2024 -0700
    add Asiatic mouflon Ovis_orientalis per user request
• src/hg/makeDb/doc/hg38/hprcInDel.txt
  • lines changed 6, context: html, text, full: html, text
    675293a87172d440c9c78b1c1bdc54610bc35a77 Tue May 7 14:14:26 2024 -0700
    changes to HPRC rearrangements track in response to SAB refs #33484
• src/hg/makeDb/doc/hg38/hprcRearrange.txt
  • lines changed 4, context: html, text, full: html, text
    675293a87172d440c9c78b1c1bdc54610bc35a77 Tue May 7 14:14:26 2024 -0700
    changes to HPRC rearrangements track in response to SAB refs #33484
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    3a53d8fc8ac71f054e07b33173831663e1145fde Wed May 8 19:11:12 2024 -0700
    adding a couple of Apodemu per user request
  • lines changed 1, context: html, text, full: html, text
    30d3d908a1cde40a5cdee48cb033474aae735fea Fri May 10 15:51:05 2024 -0700
    add Asiatic mouflon Ovis_orientalis per user request
• src/hg/makeDb/doc/pairBrowse/hg38-JAGYVI010000087.1.txt
  • lines changed 10, context: html, text, full: html, text
    3b88e1378464206ae20e4105071c3dad3697d0ad Sun May 12 14:42:19 2024 -0700
    ongoing work on pairwise browser
• src/hg/makeDb/doc/pairBrowse/hg38-JAHAOR010000021.1.txt
  • lines changed 9, context: html, text, full: html, text
    3b88e1378464206ae20e4105071c3dad3697d0ad Sun May 12 14:42:19 2024 -0700
    ongoing work on pairwise browser
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 5, context: html, text, full: html, text
    675293a87172d440c9c78b1c1bdc54610bc35a77 Tue May 7 14:14:26 2024 -0700
    changes to HPRC rearrangements track in response to SAB refs #33484
• src/hg/makeDb/trackDb/human/hg38/knownGeneV46.html
  • lines changed 3, context: html, text, full: html, text
    60351966e24ab94f207300440f795183cfa04944 Tue May 7 14:27:20 2024 -0700
    Adding back the paragraph that mentions the table that provides statistics since we are waiting for the official GENCODE release which will have the statistics, refs #33080
  • lines changed 4, context: html, text, full: html, text
    061d26ddbcbc8670769603d9be3b8ac30e574946 Wed May 8 12:06:15 2024 -0700
    Updating the paragraph regarding the statistics for the GENCODE release, refs #33080
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM35.html
  • lines changed 3, context: html, text, full: html, text
    60351966e24ab94f207300440f795183cfa04944 Tue May 7 14:27:20 2024 -0700
    Adding back the paragraph that mentions the table that provides statistics since we are waiting for the official GENCODE release which will have the statistics, refs #33080
  • lines changed 6, context: html, text, full: html, text
    061d26ddbcbc8670769603d9be3b8ac30e574946 Wed May 8 12:06:15 2024 -0700
    Updating the paragraph regarding the statistics for the GENCODE release, refs #33080
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
  • lines changed 2, context: html, text, full: html, text
    2616623a638ac5f6606049570e44f0ea040f0353 Thu May 9 08:19:37 2024 -0700
    not all liftOver chains have nets
• src/hg/utils/automation/featBitsSurvey.pl
  • lines changed 31, context: html, text, full: html, text
    1a47b6607eb6ea04f8d286f74bb1d812d7c6757c Fri May 3 16:57:20 2024 -0700
    now with common names
• src/hg/utils/buildPairAssembly/buildPairAssembly.c
  • lines changed 222, context: html, text, full: html, text
    83a03d08eb15f3352267026c3d875e2f8ff68bd0 Wed May 8 16:09:49 2024 -0700
    a utility to build an assembly hub for a sequence that includes both sequences from a pairwise alignment
  • lines changed 78, context: html, text, full: html, text
    a94ab9b578fa7ff2bad82cefb1742985c55b6a76 Thu May 9 15:03:10 2024 -0700
    ongoing work on pair browser
• src/hg/utils/buildPairAssembly/makePair
  • lines changed 85, context: html, text, full: html, text
    3b88e1378464206ae20e4105071c3dad3697d0ad Sun May 12 14:42:19 2024 -0700
    ongoing work on pairwise browser
• src/hg/utils/buildPairAssembly/makefile
  • lines changed 3, context: html, text, full: html, text
    83a03d08eb15f3352267026c3d875e2f8ff68bd0 Wed May 8 16:09:49 2024 -0700
    a utility to build an assembly hub for a sequence that includes both sequences from a pairwise alignment
• src/hg/utils/chainArrangeCollect/chainArrangeCollect.c
  • lines changed 1, context: html, text, full: html, text
    675293a87172d440c9c78b1c1bdc54610bc35a77 Tue May 7 14:14:26 2024 -0700
    changes to HPRC rearrangements track in response to SAB refs #33484
• src/hg/utils/chainInDel/chainInDel.c
  • lines changed 1, context: html, text, full: html, text
    675293a87172d440c9c78b1c1bdc54610bc35a77 Tue May 7 14:14:26 2024 -0700
    changes to HPRC rearrangements track in response to SAB refs #33484
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    5a48c29d628d7e98d2166bf612c2301b247d9189 Mon May 13 10:35:54 2024 -0700
    New version number v465
• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
  • lines changed 11, context: html, text, full: html, text
    fc87e789d56a5ba55444baa6f20a222aebaa5cd5 Mon May 13 02:42:33 2024 -0700
    added option to bigWigAverageOverBed to output TSV headers
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    5ed05207826660a85163b39177004b7e85aeea24 Mon May 13 10:09:05 2024 -0700
    v465 preview2, refs #33577
  • lines changed 3, context: html, text, full: html, text
    ec82913fbd995daa808b855af06d40295abbb49b Mon May 13 10:35:09 2024 -0700
    v465 final build, refs #33577

• lines changed: 1153
• files changed: 43