All File Changes

v489_preview to v489_preview2 (2025-09-29 to 2025-10-06) v489

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    929bf2136f6b12ad81e170c68ec982909c473ba6 Wed Oct 1 16:41:33 2025 -0700
    Let auth table name for apiKeys be configued in hg.conf, refs #36428
  • lines changed 1, context: html, text, full: html, text
    fc41b9864400d6030806ea0188221ed0646cb28a Fri Oct 3 16:48:20 2025 -0700
    Adding a line break so the API key doesn't show up just below the text, refs #36428
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 5, context: html, text, full: html, text
    929bf2136f6b12ad81e170c68ec982909c473ba6 Wed Oct 1 16:41:33 2025 -0700
    Let auth table name for apiKeys be configued in hg.conf, refs #36428
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    e9d19ac44bb91c8382ea2e0eed7f28799ebb032f Thu Oct 2 13:28:26 2025 -0700
    Updating the name of the button that hides all tracks in the group, refs #36354
• src/hg/htdocs/goldenPath/help/hubBasics.html
  • lines changed 29, context: html, text, full: html, text
    8ad25cfae7edef1204463a4fac2f844ed18d8436 Wed Oct 1 17:09:06 2025 -0700
    adding a toc, making links absolute, and some other fixes based on code review, refs #36443
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 444, context: html, text, full: html, text
    6bfdbe4ecaaf5cbc14f3811873696bfe9bdbee05 Fri Oct 3 17:08:00 2025 -0700
    Updating the poster gallery and incorporating teams feedback, refs #36182
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    7864b9423672476a19fa8d52d7801504f309afe9 Tue Sep 30 15:10:50 2025 -0700
    Updating the long/short label for the long-read variants container. Updating the announcement for CoLoRSdb to reflect this change, refs #34120
• src/hg/hubApi/apiUtils.c
  • lines changed 1, context: html, text, full: html, text
    b7ca6a235122ec881dcdb6951fe3fc1fcab49acd Wed Oct 1 09:37:20 2025 -0700
    fixing error 500 on /list/files in the API, no ticket number yet as this is a build patch which requires a commit-ID
• src/hg/hubApi/list.c
  • lines changed 1, context: html, text, full: html, text
    b7ca6a235122ec881dcdb6951fe3fc1fcab49acd Wed Oct 1 09:37:20 2025 -0700
    fixing error 500 on /list/files in the API, no ticket number yet as this is a build patch which requires a commit-ID
• src/hg/inc/hubSpaceKeys.h
  • lines changed 1, context: html, text, full: html, text
    929bf2136f6b12ad81e170c68ec982909c473ba6 Wed Oct 1 16:41:33 2025 -0700
    Let auth table name for apiKeys be configued in hg.conf, refs #36428
• src/hg/js/autocompleteCat.js
  • lines changed 4, context: html, text, full: html, text
    e986a0d4e9eac49158dc152a7d6d5ac96823b825 Tue Sep 30 14:05:11 2025 -0700
    Another spot to remove 0 len chars, this time in the autocomplete lib, refs #36387
• src/hg/lib/botDelay.c
  • lines changed 28, context: html, text, full: html, text
    b74aa56e4115f371dbe818e98412f0c9e738e142 Tue Sep 30 07:45:16 2025 -0700
    allow apiKey=xxx to get around captcha and also bottleneck on the apiKey then, not on the cookie userId or hgsid, refs #36428
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    7b28a28c6769f74499a7cc7e5a54028b49dad51c Tue Sep 30 06:00:10 2025 -0700
    making sure that the user cannot have a verbose variable stuck in their cart. Also making the connection message a little shorter. refs #36426
  • lines changed 7, context: html, text, full: html, text
    b74aa56e4115f371dbe818e98412f0c9e738e142 Tue Sep 30 07:45:16 2025 -0700
    allow apiKey=xxx to get around captcha and also bottleneck on the apiKey then, not on the cookie userId or hgsid, refs #36428
• src/hg/lib/hubSpaceKeys.c
  • lines changed 3, context: html, text, full: html, text
    929bf2136f6b12ad81e170c68ec982909c473ba6 Wed Oct 1 16:41:33 2025 -0700
    Let auth table name for apiKeys be configued in hg.conf, refs #36428
• src/hg/makeDb/trackDb/evaSnp.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/colorsDb.html
  • lines changed 62, context: html, text, full: html, text
    20efabed0ba5f49fa77d9a6839c552935c8efe55 Wed Oct 1 16:45:11 2025 -0700
    Making changes based on code review feedback. Fixing typos, making references in alphabetical order, and other small changes. refs #36440
• src/hg/makeDb/trackDb/human/colorsDb.ra
  • lines changed 5, context: html, text, full: html, text
    7864b9423672476a19fa8d52d7801504f309afe9 Tue Sep 30 15:10:50 2025 -0700
    Updating the long/short label for the long-read variants container. Updating the announcement for CoLoRSdb to reflect this change, refs #34120
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/gnomad.pext.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.new.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/varFreqs.html
  • lines changed 23, context: html, text, full: html, text
    173f5b2e4df55dd4c898ee49d53b1588c9d8dd4d Thu Oct 2 14:53:12 2025 -0700
    Sorting the references section by alphabetical order. Using the HTML entity for the right arrow. Using lowercase for 'help page'. refs #36259
• src/hg/makeDb/trackDb/human/longReadVariants.html
  • lines changed 1, context: html, text, full: html, text
    7864b9423672476a19fa8d52d7801504f309afe9 Tue Sep 30 15:10:50 2025 -0700
    Updating the long/short label for the long-read variants container. Updating the announcement for CoLoRSdb to reflect this change, refs #34120
  • lines changed 6, context: html, text, full: html, text
    da9a225ac1d17c6c6659209c0dfb4534e6ab51d7 Tue Sep 30 16:16:07 2025 -0700
    Fixing a typo in CoLoRSdb (missing S). Bolding the track names. Using lowercase s in 'small' and 'structural', refs #34120
• src/hg/makeDb/trackDb/human/longReadVariants.ra
  • lines changed 1, context: html, text, full: html, text
    d90a01c5f485f380e16c450eb985400d1f5d0af2 Wed Oct 1 17:03:46 2025 -0700
    Updating the ra file for the long-read variants since it isn't just about colorsdb, refs #36440
• src/hg/makeDb/trackDb/human/mitoMap.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    7b34df1cd22e7187feff14f87d2570a9c12c71ab Wed Oct 1 17:05:13 2025 -0700
    Upating the include for the colorsdb.ra name change to longReadVariants.ra, refs #36440
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra
  • lines changed 1, context: html, text, full: html, text
    9bcc94852decce3f6cfb9b14a6c8af649a92c7d2 Thu Oct 2 12:11:51 2025 -0700
    Squashing old pennantIcons.
• src/inc/bigWig.h
  • lines changed 7, context: html, text, full: html, text
    bc587fd886e5c5973d56b138aece47f34857e7eb Sat Oct 4 21:36:04 2025 -0700
    added -bed option to bigWigToWig to selectively output wiggle regions (contributed by Michael Hiller)
• src/lib/bwgQuery.c
  • lines changed 173, context: html, text, full: html, text
    bc587fd886e5c5973d56b138aece47f34857e7eb Sat Oct 4 21:36:04 2025 -0700
    added -bed option to bigWigToWig to selectively output wiggle regions (contributed by Michael Hiller)
• src/product/installer/browserSetup.sh
  • lines changed 12, context: html, text, full: html, text
    03566d28af0d1630cec3eaae5dd278df3648f074 Tue Sep 30 05:43:28 2025 -0700
    removing hgdownload-euro from installer script, no ML ticket yet
• src/product/mirrorManual.txt
  • lines changed 1, context: html, text, full: html, text
    c2c93e82ecbae0efba902ff1c39c1a1b0b0c50da Tue Sep 30 11:23:08 2025 -0700
    Forgot to update the mirrorManual.txt instead of mirrorManual.html, refs #34740
• src/utils/bigWigToWig/bigWigToWig.c
  • lines changed 54, context: html, text, full: html, text
    bc587fd886e5c5973d56b138aece47f34857e7eb Sat Oct 4 21:36:04 2025 -0700
    added -bed option to bigWigToWig to selectively output wiggle regions (contributed by Michael Hiller)
• src/utils/qa/qaTestScript.py
  • lines changed 50, context: html, text, full: html, text
    fb5d68cdc0a920f47900f319c54a956384c8ee09 Mon Sep 29 18:39:55 2025 -0700
    Improving the hgLiftOver test mouseover menu interaction and updating the cartReset with a direct URL, No RM

• lines changed: 944
• files changed: 45