All File Changes

v481_preview to v481_preview2 (2025-04-14 to 2025-04-21) v481

• confs/hgwbeta.hg.conf
  • lines changed 13, context: html, text, full: html, text
    d505b3f5a263432a2dc11b17b86f50b45a253614 Sun Apr 20 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgCustom/hgCustom.c
  • lines changed 7, context: html, text, full: html, text
    e10d4e543c21831fa3bdc8fb515de9eb2411223b Mon Apr 14 23:15:21 2025 -0700
    Fixing instructions in hgCustom for URL-only custom tracks. fixes #20985.
  • lines changed 14, context: html, text, full: html, text
    2e51ddb856d99b25998ea2b75907103d15b1ff6c Tue Apr 15 12:31:02 2025 -0700
    Makes configuration instructions for URL-only custom tracks very obvious with red message at the top. refs #20985
• src/hg/hgGateway/hgGateway.html
  • lines changed 1, context: html, text, full: html, text
    6390a9da95b821f671617bbb5a7c4f64de4ae355 Mon Apr 21 09:58:01 2025 -0700
    Assigning an id to the assemblySearch.html anchor element for the interactive Gateway tutorial, refs #35464
• src/hg/hgGene/hgGene.c
  • lines changed 6, context: html, text, full: html, text
    88a4d68261b55e8c277557b13c60740a95ace103 Mon Apr 14 15:03:38 2025 -0700
    support knownGene track with quickLift
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 13, context: html, text, full: html, text
    c1f214b4ddd63132bbbc2e12e55d37b2fe20a3a0 Thu Apr 17 16:04:24 2025 -0700
    When a user hits an error during upload, we need to remove the temp file created by tusd to allow the user to re-try the upload again, refs Max zoom
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    a3fb7947061065fd8f2fb5ead75ba43d72a74229 Wed Apr 16 20:20:47 2025 -0700
    Fixes hgTables Table Browser filter error caused by not handling special case of tables with both db table and bigGenePred or bigBed. This now works correctly. fixes #31105
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 2, context: html, text, full: html, text
    dce0d45176ae568f343e169091d827841818f8bb Mon Apr 14 16:06:01 2025 -0700
    Fixing contact URL because of a typo (missing contacts.html not contact.html), no Redmine
  • lines changed 10, context: html, text, full: html, text
    1a3c324b528c57e4b6211d872a3b4e666b032259 Mon Apr 14 16:27:03 2025 -0700
    Adding function for listing GenArk genomes, refs #32897
  • lines changed 1, context: html, text, full: html, text
    4bb6e6a20045411de707cf68183e150e78b82396 Mon Apr 14 16:35:16 2025 -0700
    Adding the optional 'maxItemsOutput' to the optional parameters for genarkGenomes, refs #32897
• src/hg/js/hgMyData.js
  • lines changed 2, context: html, text, full: html, text
    bd24e0ba0761ae6a1a5a245a16aa024db6d2235d Thu Apr 17 15:19:35 2025 -0700
    Adjust hubspace columns when a file is added and when showing the page on reload
• src/hg/lib/encode4.as
  • lines changed 24, context: html, text, full: html, text
    8f6b3fb20ce624a7efbae0d9a84f10ee7e06c885 Wed Apr 16 18:20:07 2025 -0700
    Adding encode4 track #31368. Should probably be renamed.
• src/hg/lib/hgncBig62.as
  • lines changed 2, context: html, text, full: html, text
    5961996f55b3fff34f0c9e145abe88317be132a0 Fri Apr 18 16:40:00 2025 -0700
    refs #34754
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    019341f44cfc8fe9619366bff4d04e15233dd6a8 Fri Apr 18 16:17:45 2025 -0700
    Fix invalid tag in filterBy <select> html. Select can only contain option, optgroup, or hr children, so stuffing a br in there like we were doing was throwing off later dropdownchecklist code that relies on the first child to be an option or optgroup. But only in Chrome as Chrome is more lenient and tolerates invalid tags in selects, refs #35529
• src/hg/lib/recount3.as
  • lines changed 18, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 8, context: html, text, full: html, text
    80044a35a11a2b28765d2db6a85b86e792ce65cf Tue Apr 15 12:12:01 2025 -0700
    VGP update stragglers refs #29545
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 2, context: html, text, full: html, text
    967e15b3e2949b32f3874695b94b55f8923d3c15 Mon Apr 14 14:12:02 2025 -0700
    use gbdb URL instead of h/ link to avoid week delay for assembly to show up in hgcentral table refs #34370
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 225, context: html, text, full: html, text
    d2658ef3f0b1d84dc3dfc0058fa9c67219557db3 Tue Apr 15 10:24:59 2025 -0700
    BRC update adding missing items
• src/hg/makeDb/doc/hg19.txt
  • lines changed 77, context: html, text, full: html, text
    00a42f1666c47609c7655b9de0d0959dd5706745 Fri Apr 18 00:21:59 2025 -0700
    Added strand to HGNC and fetching lastest data for hg19. fixes #34754.
• src/hg/makeDb/doc/hg38/hgnc.txt
  • lines changed 96, context: html, text, full: html, text
    9bc58d46a3c3ac5e366392ad074baa07facb6925 Thu Apr 17 23:34:56 2025 -0700
    Added strand to HGNC and fetching lastest data. refs #34754.
• src/hg/makeDb/doc/hg38/recount3.txt
  • lines changed 61, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    bc708303c647a544ce8401c2d376f282d906b387 Tue Apr 15 15:31:45 2025 -0700
    VGP update refs #34370
• src/hg/makeDb/doc/mm10.txt
  • lines changed 55, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
  • lines changed 47, context: html, text, full: html, text
    8f6b3fb20ce624a7efbae0d9a84f10ee7e06c885 Wed Apr 16 18:20:07 2025 -0700
    Adding encode4 track #31368. Should probably be renamed.
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 52, context: html, text, full: html, text
    3ef4f1ee9a45852fd9bfc625bc01cea6c9981367 Wed Apr 16 13:38:00 2025 -0700
    VGP update refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    3ef4f1ee9a45852fd9bfc625bc01cea6c9981367 Wed Apr 16 13:38:00 2025 -0700
    VGP update refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 33, context: html, text, full: html, text
    3ef4f1ee9a45852fd9bfc625bc01cea6c9981367 Wed Apr 16 13:38:00 2025 -0700
    VGP update refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 79, context: html, text, full: html, text
    3ef4f1ee9a45852fd9bfc625bc01cea6c9981367 Wed Apr 16 13:38:00 2025 -0700
    VGP update refs #34370
• src/hg/makeDb/outside/recount3/junctionsToBed.py
  • lines changed 125, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
• src/hg/makeDb/trackDb/human/cadd1_7.ra
  • lines changed 4, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/decipher.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 2, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV47lift37.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg38/encode4.html
  • lines changed 4, context: html, text, full: html, text
    8f6b3fb20ce624a7efbae0d9a84f10ee7e06c885 Wed Apr 16 18:20:07 2025 -0700
    Adding encode4 track #31368. Should probably be renamed.
• src/hg/makeDb/trackDb/human/hg38/encode4.ra
  • lines changed 1, context: html, text, full: html, text
    8f6b3fb20ce624a7efbae0d9a84f10ee7e06c885 Wed Apr 16 18:20:07 2025 -0700
    Adding encode4 track #31368. Should probably be renamed.
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
  • lines changed 3, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 4, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 2, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg38/recount3.ra
  • lines changed 76, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 5, context: html, text, full: html, text
    97e747a3f4878db6cccea52e92c5636194d24ee6 Wed Apr 16 09:44:22 2025 -0700
    clarifying that 447 zoonomia includes primates
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    28e6773e9bfa82b6fa008363bba841066915c3f1 Wed Apr 16 08:32:20 2025 -0700
    adding HAR track for Katie Pollard to review
  • lines changed 2, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
  • lines changed 5, context: html, text, full: html, text
    8f6b3fb20ce624a7efbae0d9a84f10ee7e06c885 Wed Apr 16 18:20:07 2025 -0700
    Adding encode4 track #31368. Should probably be renamed.
  • lines changed 15, context: html, text, full: html, text
    1ad7922878c53ea7aa6b3bda34a251c016f43295 Fri Apr 18 04:20:54 2025 -0700
    adding ultras from hirams hub, no redmine yet
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV47.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/hs1/problematic.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 2, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/mouse/mm10/recount3.ra
  • lines changed 21, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
  • lines changed 4, context: html, text, full: html, text
    8f6b3fb20ce624a7efbae0d9a84f10ee7e06c885 Wed Apr 16 18:20:07 2025 -0700
    Adding encode4 track #31368. Should probably be renamed.
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM36.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/makeDb/trackDb/recount3.html
  • lines changed 81, context: html, text, full: html, text
    8e2ce67692e814db90b2d2938915712ff9b0ee51 Wed Apr 16 18:07:03 2025 -0700
    Adding recount3 #34886
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 1, context: html, text, full: html, text
    032f71725a8af7b83496a5fef12ca0f1123cbead Tue Apr 15 16:39:19 2025 -0700
    Squashing stale pennanticons.
• src/hg/utils/automation/updateName2.pl
  • lines changed 7, context: html, text, full: html, text
    a086cac4d10bed4ed39ae97ce76f5756c2ee5b17 Tue Apr 15 15:23:46 2025 -0700
    mito genes do not have the extra info fields refs #34370
• src/hg/utils/otto/panelApp/genes.py
  • lines changed 8, context: html, text, full: html, text
    5723e5d95d264e4a3eb6d2a36b519b177608f5fe Tue Apr 15 09:16:34 2025 -0700
    Fixing an infinte loop bug: Moving sleep and counter outside of the exception block so the count also increments during the else statement. Adding a message to the assert(False) line. No Remdmine.
  • lines changed 1, context: html, text, full: html, text
    abea526d50eb92c5e27a5c19051749d87a4a78f5 Tue Apr 15 11:20:55 2025 -0700
    Updating the URL to match the new styling from PanelApp, no Redmine.
  • lines changed 1, context: html, text, full: html, text
    e01154e5326c5b380ba1af9c8b74a2011c1ec525 Tue Apr 15 11:58:31 2025 -0700
    Forgot to add the ? to specify the parameters for the panelApp otto, no Redmine.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    e8405f0a3004ccb304cd7b061b9b94d63d29197f Sat Apr 19 19:12:00 2025 -0700
    Exit non-zero if an error occurs creating the bigBed. Enhance test to check exit code for error cases #35551
• src/utils/bedToBigBed/tests/expected/test2bitMissingSeq.err
  • lines changed 1, context: html, text, full: html, text
    e8405f0a3004ccb304cd7b061b9b94d63d29197f Sat Apr 19 19:12:00 2025 -0700
    Exit non-zero if an error occurs creating the bigBed. Enhance test to check exit code for error cases #35551
• src/utils/bedToBigBed/tests/input/fakeGenome.fa
  • lines changed 4, context: html, text, full: html, text
    e8405f0a3004ccb304cd7b061b9b94d63d29197f Sat Apr 19 19:12:00 2025 -0700
    Exit non-zero if an error occurs creating the bigBed. Enhance test to check exit code for error cases #35551
• src/utils/bedToBigBed/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    e8405f0a3004ccb304cd7b061b9b94d63d29197f Sat Apr 19 19:12:00 2025 -0700
    Exit non-zero if an error occurs creating the bigBed. Enhance test to check exit code for error cases #35551
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    e5d0c0cb597fb3c6cc1bc061e59b206003f9ba5c Mon Apr 21 10:44:20 2025 -0700
    v481 preview2, refs #35512

• lines changed: 1306
• files changed: 69