All File Changes

v491_base to v492_preview (2025-11-24 to 2025-12-01) v492

• confs/hgwbeta.hg.conf
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    40df4522cde73e8a0046a1358d04320e2d254f86 Sun Nov 30 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• docs/gb101.md
  • lines changed 1, context: html, text, full: html, text
    724b13dc3e31de4c791108908e12925c992d9145 Mon Dec 1 13:05:51 2025 -0800
    Adding the db= parameter to fix a bug if the user clicked the button while viewing a hub, no Redmine.
• src/hg/hgCustom/hgCustom.c
  • lines changed 14, context: html, text, full: html, text
    f69a8b38592faaedf9c6f254ce5d56e73d91ac64 Tue Sep 30 10:48:18 2025 -0700
    Initial commit of the customTrack tutorial, refs #34354
  • lines changed 18, context: html, text, full: html, text
    984a3761c1300e20e463304a81098b312da7bd66 Wed Nov 26 15:49:51 2025 -0800
    Adding the custom track tutorial, refs #34354
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 1, context: html, text, full: html, text
    b4ecdd4d8460be76fec8cc30bd300ef449cc6fac Mon Nov 24 15:11:14 2025 -0800
    Show a warning message when a user tries hubspace on genome-euro or genome-asia telling them to try on US server. This is a temporary measure until we can add a special workaround to get around the captcha from client code, refs #36290
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 31, context: html, text, full: html, text
    8295800d611b301861e0b6e8597e856ae96abf78 Mon Nov 24 16:19:31 2025 -0800
    successful HGVS searches get saved into the 'recent searches' dropdown on hgTracks. the position box tries to suggest hgvs when the search term is longer than 8 characters, otherwise we assume it's a gene, refs #35984
• src/hg/hgTables/mainPage.c
  • lines changed 4, context: html, text, full: html, text
    4140d0e2412d8edb63d1aaac196f6c98612f3328 Fri Nov 21 16:52:25 2025 -0800
    Add hgTables Summary and intersection buttons for knownCanonical. refs #rm36524
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    7412238abe94bb147ccb3570d4766d8bc063dbfe Mon Nov 24 13:05:48 2025 -0800
    debug cleanup
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 4, context: html, text, full: html, text
    5ed8f560efb5af18673ae76180e24ec493698cb2 Thu Nov 20 17:07:25 2025 -0800
    Fixes pdf output problem. We set hgFindMatches = NULL for pdf output to suppress the item search highlight. But loading in bigBedTrack and squishPackyMode both depend on that search term, so we cannot just set it to NULL. A copy of it called origHgFindMatches exists and is available to those routines that need the original search value.
• src/hg/hgTracks/chromGraphTrack.c
  • lines changed 1, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/decorator.c
  • lines changed 1, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/encode.c
  • lines changed 1, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 2, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    5ed8f560efb5af18673ae76180e24ec493698cb2 Thu Nov 20 17:07:25 2025 -0800
    Fixes pdf output problem. We set hgFindMatches = NULL for pdf output to suppress the item search highlight. But loading in bigBedTrack and squishPackyMode both depend on that search term, so we cannot just set it to NULL. A copy of it called origHgFindMatches exists and is available to those routines that need the original search value.
  • lines changed 2, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    5ed8f560efb5af18673ae76180e24ec493698cb2 Thu Nov 20 17:07:25 2025 -0800
    Fixes pdf output problem. We set hgFindMatches = NULL for pdf output to suppress the item search highlight. But loading in bigBedTrack and squishPackyMode both depend on that search term, so we cannot just set it to NULL. A copy of it called origHgFindMatches exists and is available to those routines that need the original search value.
• src/hg/hgTracks/imageV2.c
  • lines changed 25, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/imageV2.h
  • lines changed 7, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    5ed8f560efb5af18673ae76180e24ec493698cb2 Thu Nov 20 17:07:25 2025 -0800
    Fixes pdf output problem. We set hgFindMatches = NULL for pdf output to suppress the item search highlight. But loading in bigBedTrack and squishPackyMode both depend on that search term, so we cannot just set it to NULL. A copy of it called origHgFindMatches exists and is available to those routines that need the original search value.
  • lines changed 6, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/variation.c
  • lines changed 1, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/inc/hgFind.h
  • lines changed 11, context: html, text, full: html, text
    8295800d611b301861e0b6e8597e856ae96abf78 Mon Nov 24 16:19:31 2025 -0800
    successful HGVS searches get saved into the 'recent searches' dropdown on hgTracks. the position box tries to suggest hgvs when the search term is longer than 8 characters, otherwise we assume it's a gene, refs #35984
• src/hg/js/autocomplete.js
  • lines changed 25, context: html, text, full: html, text
    8295800d611b301861e0b6e8597e856ae96abf78 Mon Nov 24 16:19:31 2025 -0800
    successful HGVS searches get saved into the 'recent searches' dropdown on hgTracks. the position box tries to suggest hgvs when the search term is longer than 8 characters, otherwise we assume it's a gene, refs #35984
• src/hg/js/hgCustom.js
  • lines changed 5, context: html, text, full: html, text
    f69a8b38592faaedf9c6f254ce5d56e73d91ac64 Tue Sep 30 10:48:18 2025 -0700
    Initial commit of the customTrack tutorial, refs #34354
  • lines changed 17, context: html, text, full: html, text
    984a3761c1300e20e463304a81098b312da7bd66 Wed Nov 26 15:49:51 2025 -0800
    Adding the custom track tutorial, refs #34354
• src/hg/js/hgMyData.js
  • lines changed 2, context: html, text, full: html, text
    b4ecdd4d8460be76fec8cc30bd300ef449cc6fac Mon Nov 24 15:11:14 2025 -0800
    Show a warning message when a user tries hubspace on genome-euro or genome-asia telling them to try on US server. This is a temporary measure until we can add a special workaround to get around the captcha from client code, refs #36290
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    8295800d611b301861e0b6e8597e856ae96abf78 Mon Nov 24 16:19:31 2025 -0800
    successful HGVS searches get saved into the 'recent searches' dropdown on hgTracks. the position box tries to suggest hgvs when the search term is longer than 8 characters, otherwise we assume it's a gene, refs #35984
  • lines changed 5, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/js/tutorials/customTrackTutorial.js
  • lines changed 71, context: html, text, full: html, text
    f69a8b38592faaedf9c6f254ce5d56e73d91ac64 Tue Sep 30 10:48:18 2025 -0700
    Initial commit of the customTrack tutorial, refs #34354
  • lines changed 45, context: html, text, full: html, text
    ea778c06746a6f023fb1f6e8409a36c073876c38 Fri Oct 31 17:22:53 2025 -0700
    Adding some steps but not done yet
  • lines changed 326, context: html, text, full: html, text
    984a3761c1300e20e463304a81098b312da7bd66 Wed Nov 26 15:49:51 2025 -0800
    Adding the custom track tutorial, refs #34354
  • lines changed 17, context: html, text, full: html, text
    148452cbb04d1585ca0efb73cff479ccba0ea9d1 Wed Nov 26 16:46:58 2025 -0800
    Making edits based on Lou's feedback, refs #34354
• src/hg/js/tutorials/makefile
  • lines changed 1, context: html, text, full: html, text
    f69a8b38592faaedf9c6f254ce5d56e73d91ac64 Tue Sep 30 10:48:18 2025 -0700
    Initial commit of the customTrack tutorial, refs #34354
• src/hg/js/tutorials/tutorialPopup.js
  • lines changed 21, context: html, text, full: html, text
    984a3761c1300e20e463304a81098b312da7bd66 Wed Nov 26 15:49:51 2025 -0800
    Adding the custom track tutorial, refs #34354
  • lines changed 4, context: html, text, full: html, text
    e3e6c0f4df0c5b580fb65d02738b92217fcea1dc Mon Dec 1 12:14:41 2025 -0800
    Using the wrong database, hg38, and the tutorial should use hg19, refs #34354
  • lines changed 1, context: html, text, full: html, text
    f5b23e253e246d827101c372a3f70aa778995871 Mon Dec 1 12:26:04 2025 -0800
    Updating the text since this tutorial is only available on hg19, refs #34354
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    c32d6e08d19a0b8ad7ece12aab39d0ba0be7a9e1 Mon Dec 1 16:26:27 2025 -0800
    hgTracks tooltips use the data-tooltip attribute on the area element if present, falling back to the title attribute. Makes title attributes for (hopefully all) tracks with special tooltips put the tooltip string into the data-tooltip attribute instead of the title attribute, refs #35756
• src/hg/lib/hgFind.c
  • lines changed 2, context: html, text, full: html, text
    8295800d611b301861e0b6e8597e856ae96abf78 Mon Nov 24 16:19:31 2025 -0800
    successful HGVS searches get saved into the 'recent searches' dropdown on hgTracks. the position box tries to suggest hgvs when the search term is longer than 8 characters, otherwise we assume it's a gene, refs #35984
  • lines changed 12, context: html, text, full: html, text
    8021b64b107e40cdbd45c2b76989bd61969205ed Tue Nov 25 12:09:58 2025 -0800
    Make hgvs searches highlight the ncbiRefSeqSelect table if that transcript is in there instead of the larger ncbiRefSeqCurated table. Fall back to ncbiRefSeqCurated, refs #36201
• src/hg/lib/trackHub.c
  • lines changed 11, context: html, text, full: html, text
    4165c886d31e4e347d85e0fc134fc085af2bf31f Mon Nov 24 13:51:31 2025 -0800
    Fixes the concern where externally loaded non-local-hubs might want to use protected local bigDataUrls such as /gbdb/hg38/bbi/hgmd.bb, which will now be forbidden when loading the tracks. Tells the user which setting has the invalid url and that such usage is not allowed. It also supports udc.localDir setting for GBIB and mirrors. As usual that should be set carefully as mentioned in the ticket, and also provides a way to test with and without udc.localDir allowing paths. refs #34544
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    bd6a4bc4fe15cc6ba1353603df2c9c4278c75160 Fri Nov 28 23:18:35 2025 -0800
    recent user request updates refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    bd6a4bc4fe15cc6ba1353603df2c9c4278c75160 Fri Nov 28 23:18:35 2025 -0800
    recent user request updates refs #29545
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 5, context: html, text, full: html, text
    ef63626263c7b8d43c6820ff158490f4e0d8a616 Tue Nov 25 08:59:03 2025 -0800
    adding track docs to previous commit
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    bd6a4bc4fe15cc6ba1353603df2c9c4278c75160 Fri Nov 28 23:18:35 2025 -0800
    recent user request updates refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    bd6a4bc4fe15cc6ba1353603df2c9c4278c75160 Fri Nov 28 23:18:35 2025 -0800
    recent user request updates refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    bd6a4bc4fe15cc6ba1353603df2c9c4278c75160 Fri Nov 28 23:18:35 2025 -0800
    recent user request updates refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    bd6a4bc4fe15cc6ba1353603df2c9c4278c75160 Fri Nov 28 23:18:35 2025 -0800
    recent user request updates refs #29545
• src/hg/makeDb/scripts/finngen_to_vcf.py
  • lines changed 249, context: html, text, full: html, text
    85a3ec13e80a0e61f16e691afb878956e0483892 Fri Nov 28 08:53:18 2025 -0800
    adding Finnland to var freqs track, refs #36642
• src/hg/makeDb/trackDb/human/hg38/ancient.ra
  • lines changed 2, context: html, text, full: html, text
    84e463a4d1ce0d4dc03c97224f235fad65e0f4f4 Mon Dec 1 08:32:03 2025 -0800
    adding parent track docs to subtracks, refs #36586
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    3d416983a22ec1b123e9951e3511cdcec36df0b2 Mon Dec 1 15:20:30 2025 -0800
    More feedback from Zhiping, refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra
  • lines changed 174, context: html, text, full: html, text
    3d416983a22ec1b123e9951e3511cdcec36df0b2 Mon Dec 1 15:20:30 2025 -0800
    More feedback from Zhiping, refs #34109
• src/hg/makeDb/trackDb/human/phasedVars.html
  • lines changed 183, context: html, text, full: html, text
    d7817fcecf25ab8669176afc941cadd468729f4a Tue Nov 25 08:57:14 2025 -0800
    adding Singapore to variant frequencies track
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 152, context: html, text, full: html, text
    d7817fcecf25ab8669176afc941cadd468729f4a Tue Nov 25 08:57:14 2025 -0800
    adding Singapore to variant frequencies track
  • lines changed 36, context: html, text, full: html, text
    85a3ec13e80a0e61f16e691afb878956e0483892 Fri Nov 28 08:53:18 2025 -0800
    adding Finnland to var freqs track, refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 11, context: html, text, full: html, text
    d7817fcecf25ab8669176afc941cadd468729f4a Tue Nov 25 08:57:14 2025 -0800
    adding Singapore to variant frequencies track
  • lines changed 13, context: html, text, full: html, text
    85a3ec13e80a0e61f16e691afb878956e0483892 Fri Nov 28 08:53:18 2025 -0800
    adding Finnland to var freqs track, refs #36642
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    a35bd5603343fd35129bca74f979310e4368dd13 Mon Dec 1 08:09:21 2025 -0800
    fixing tdb error
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 58, context: html, text, full: html, text
    aaec16b62487ea4d0a0c19193428917e095c756b Tue Nov 25 14:10:47 2025 -0800
    Updating the clinVarToBed script to match the one the one that is running on dev, no Redmine
• src/hg/utils/otto/genArk/devList.sh
  • lines changed 1, context: html, text, full: html, text
    54bafa77fa2deb567b4e8b1dc7bee6f5e686eb16 Mon Nov 24 12:09:41 2025 -0800
    incorrect name on the dev.today.liftOverList they were not going out refs #35575
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    89293f440067bbdd4e9473a7a86f5aff761d2b2e Tue Nov 25 14:06:09 2025 -0800
    Updating otto crontab, no Redmine.
• src/utils/qa/pairLastzWrapper.py
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    742f49971278e8b13c9d6bfef8be97263eae84d1 Tue Nov 25 16:44:28 2025 -0800
    Updating the pairLastzWrapper.py script so it can generate liftOver files for the older assemblies. Previously, you would get a message saying the assembly was suppressed since it could not determine the clade using the file given (all.*.today), refs #36712 #33200
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    54d2ab3bc67708e54ef4ce54b0bd94927e1ff18b Tue Nov 25 16:57:38 2025 -0800
    Curling the URL like Hiram recommended. Using the file from /hive was not the most up-to-date, refs #36712 #33200

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• files changed: 63