All File Changes

v484_preview to v484_preview2 (2025-06-16 to 2025-06-23) v484

• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 23, context: html, text, full: html, text
    820942c0afc0ae38edd25f8815a3df974f259cb6 Tue Jun 17 09:55:58 2025 -0700
    Removing visible ADGC7_C_17 tags that explain Column/Row source of WUSTL milestones to source XLS (these may all change after NIMH review)
  • lines changed 14, context: html, text, full: html, text
    9d55d0cd6fb98685b90c148329f789308faf050f Wed Jun 18 19:20:45 2025 -0700
    Removing visible ADGC6_ tags identifiying col/row of .xls source doc (entries may change after NIMH review) SING
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    b8aea5bf5b28fc6430dac4b3b301253188e52310 Fri Jun 20 06:42:00 2025 -0700
    added help note after intersect button, refs #34110
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    b781052c921172ea50522fb2dac418337c79fd83 Mon Jun 23 09:38:53 2025 -0700
    don't filter on 'm' for bedMethyl
• src/hg/htdocs/goldenPath/help/docker.html
  • lines changed 4, context: html, text, full: html, text
    b4cbd94c19445de87aea4ed3defbaa7c288e78e9 Thu Jun 19 09:50:42 2025 -0700
    Clarifying what is needed to enable the default cart feature. We were missing the hg.conf statement, and also adding the statement to our file of all the possible statements, refs #35862
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    487b850e5dbc6e21882e790614aaecfde9236171 Thu Jun 19 13:21:35 2025 -0700
    Feedback from CR, refs #35930
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    bb113eaa1fe0e8b96299c8e670b03c2180af94d6 Wed Jun 18 16:40:15 2025 -0700
    Code review edits, refs #35927
• src/hg/htdocs/images/bergquist25.png
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    f763b6b740aa6f6032b803d3eab5ac2c3e554a4e Tue Jun 17 08:46:54 2025 -0700
    fixing up revel docs after email from Heidi Rehm, no redmine.
• src/hg/htdocs/indexMeetings.html
  • lines changed 1, context: html, text, full: html, text
    f66b9b0cdf55fa50d309b190b8f3137b5df39874 Thu Jun 19 11:28:08 2025 -0700
    Updating link as requested by b0b.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 6, context: html, text, full: html, text
    52b757fb2d019d4b2ea9f836bff146b1390af435 Fri Jun 20 05:31:01 2025 -0700
    tiny autocomplete change, refs #35939
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    a217902ac06d246cf240f02be103050c8e95e550 Wed Jun 18 06:38:37 2025 -0700
    no captcha for IGV, refs #35938
• src/hg/makeDb/dbDbToHubTxt/dbDbToHubTxt.c
  • lines changed 1, context: html, text, full: html, text
    44d026f9ecece467941e2de29d3050689a8492f4 Wed Jun 18 14:19:46 2025 -0700
    correct spelling of descriptionUrl refs #35898
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 169, context: html, text, full: html, text
    06620dfabbaddbf072cc7da2ed8085377a1b173b Tue Jun 17 18:43:50 2025 -0700
    domestic yak (GCA_005887515.3) to sheep(GCF_016772045.2)/goat(GCF_001704415.2) lastz/chain/net run for user, refs #35876
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    b8607bcc9e37304401155e66e3a87f8b6edc8035 Thu Jun 19 09:06:41 2025 -0700
    adding one per user request refs #29545
  • lines changed 101, context: html, text, full: html, text
    c9df6cd81ece4a167f3de03888abe3522f851abf Thu Jun 19 15:29:02 2025 -0700
    adding updated HPRC assemblies refs #35415
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 2, context: html, text, full: html, text
    359adb77c8cc1ebc8f1d8013b4d138d1311b2775 Thu Jun 19 11:17:12 2025 -0700
    correct email address in the hub.txt files
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
  • lines changed 81, context: html, text, full: html, text
    6cd7003d439b355fbb5d61f2c1b80785e85c4e0e Wed Jun 18 11:39:37 2025 -0700
    Ferret musFur1 to galGal6/mm10 lastz/chain/net run for user, refs #35916
• src/hg/makeDb/doc/hg19.txt
  • lines changed 17, context: html, text, full: html, text
    395b531075423d60f7e9abe9edd0810b1a6fc0fc Tue Jun 17 08:24:04 2025 -0700
    finishing up mutscore and mcap tracks, refs #35806, #35922
• src/hg/makeDb/doc/hg38/mutscore.txt
  • lines changed 4, context: html, text, full: html, text
    395b531075423d60f7e9abe9edd0810b1a6fc0fc Tue Jun 17 08:24:04 2025 -0700
    finishing up mutscore and mcap tracks, refs #35806, #35922
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    b8607bcc9e37304401155e66e3a87f8b6edc8035 Thu Jun 19 09:06:41 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b8607bcc9e37304401155e66e3a87f8b6edc8035 Thu Jun 19 09:06:41 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/mm10.txt
  • lines changed 82, context: html, text, full: html, text
    6cd7003d439b355fbb5d61f2c1b80785e85c4e0e Wed Jun 18 11:39:37 2025 -0700
    Ferret musFur1 to galGal6/mm10 lastz/chain/net run for user, refs #35916
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b8607bcc9e37304401155e66e3a87f8b6edc8035 Thu Jun 19 09:06:41 2025 -0700
    adding one per user request refs #29545
  • lines changed 101, context: html, text, full: html, text
    c9df6cd81ece4a167f3de03888abe3522f851abf Thu Jun 19 15:29:02 2025 -0700
    adding updated HPRC assemblies refs #35415
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • lines changed 10, context: html, text, full: html, text
    624acd88b4ea5f265652ad6703c756997ed67e0b Tue Jun 17 16:11:57 2025 -0700
    not allowing two dots anymore, always split on the first dot. If sequences include dots, must use pipe character now, no redmine yet
• src/hg/makeDb/scripts/mcap/mcapToBw.py
  • lines changed 51, context: html, text, full: html, text
    395b531075423d60f7e9abe9edd0810b1a6fc0fc Tue Jun 17 08:24:04 2025 -0700
    finishing up mutscore and mcap tracks, refs #35806, #35922
• src/hg/makeDb/trackDb/chicken/galGal7b/genArk.trackDb.ra
  • lines changed 896, context: html, text, full: html, text
    083d201617a2e46b63f16cb8ee7d977fb5a7f0be Wed Jun 18 15:00:42 2025 -0700
    initial trackDb from GenArk refs #35898
• src/hg/makeDb/trackDb/chicken/galGal7b/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    083d201617a2e46b63f16cb8ee7d977fb5a7f0be Wed Jun 18 15:00:42 2025 -0700
    initial trackDb from GenArk refs #35898
• src/hg/makeDb/trackDb/chicken/galGal7w/genArk.trackDb.ra
  • lines changed 389, context: html, text, full: html, text
    083d201617a2e46b63f16cb8ee7d977fb5a7f0be Wed Jun 18 15:00:42 2025 -0700
    initial trackDb from GenArk refs #35898
• src/hg/makeDb/trackDb/chicken/galGal7w/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    083d201617a2e46b63f16cb8ee7d977fb5a7f0be Wed Jun 18 15:00:42 2025 -0700
    initial trackDb from GenArk refs #35898
• src/hg/makeDb/trackDb/hubTxtFromGenArk.pl
  • lines changed 146, context: html, text, full: html, text
    05d27bee6baaa2a68c516dc3b2ae31841479c8e8 Wed Jun 18 13:01:40 2025 -0700
    helper script to get a hub.txt and trackDb.txt out of an existing GenArk hub refs #35898
• src/hg/makeDb/trackDb/human/hg38/unusualcons.html
  • lines changed 22, context: html, text, full: html, text
    8bfebb8961bd612d21f9f5c1144ed8eba18177b1 Tue Jun 17 13:24:24 2025 -0700
    Removing links to the papers in the description since it is against our styling suggestions. Fixing other typos found by Gerardo in code review for th Unusual Conservation track, refs #35936
• src/hg/makeDb/trackDb/human/hg38/unusualcons.ra
  • lines changed 2, context: html, text, full: html, text
    c6235f265d85c7ab55dd84b2e2d773604e3ac2ec Tue Jun 17 02:21:00 2025 -0700
    fixing incorrect bigbed sizes, refs #35703
• src/hg/makeDb/trackDb/human/mcap.ra
  • lines changed 66, context: html, text, full: html, text
    395b531075423d60f7e9abe9edd0810b1a6fc0fc Tue Jun 17 08:24:04 2025 -0700
    finishing up mutscore and mcap tracks, refs #35806, #35922
• src/hg/makeDb/trackDb/human/mutscore.ra
  • lines changed 1, context: html, text, full: html, text
    395b531075423d60f7e9abe9edd0810b1a6fc0fc Tue Jun 17 08:24:04 2025 -0700
    finishing up mutscore and mcap tracks, refs #35806, #35922
• src/hg/makeDb/trackDb/human/panelApp.alpha.ra
  • lines changed 20, context: html, text, full: html, text
    d60064988c9b779b2045522e87ed2ce7d2633a3e Thu Jun 19 18:24:21 2025 -0700
    Updated the mouseovers to use html elements such as bold and line breaks, improving readability. Also added default filters for version since I changed the track to create items from all versions, not just >.99. The Genomics England track has a default version value of 1, so even though more items are in the track the display should not be different. This change was done as recommended by the panelApp Australia collaborators, so that one displays all panels regardless of version. Refs #35758
• src/hg/makeDb/trackDb/human/panelApp.html
  • lines changed 18, context: html, text, full: html, text
    cba91350b2e4ad93790c0e76afb9b56660fb8c5a Thu Jun 19 18:25:15 2025 -0700
    Updating the desc page with the new rules used in the track generation, primarily that we are not just using versions >.99. Refs #35758
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 79, context: html, text, full: html, text
    0af931d3102ad6cca6a357e6d831774b5efaf6eb Tue Jun 17 08:02:55 2025 -0700
    fixing prediction scores track ra file, broke build
  • lines changed 20, context: html, text, full: html, text
    c613ca6dd305b556af1148511ecd737317b3fe5b Tue Jun 17 08:48:49 2025 -0700
    improving docs page of deleteriousness supertrack, no redmine, email from Heidi Rehm
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    0af931d3102ad6cca6a357e6d831774b5efaf6eb Tue Jun 17 08:02:55 2025 -0700
    fixing prediction scores track ra file, broke build
• src/hg/makeDb/trackDb/human/revel.html
  • lines changed 24, context: html, text, full: html, text
    f763b6b740aa6f6032b803d3eab5ac2c3e554a4e Tue Jun 17 08:46:54 2025 -0700
    fixing up revel docs after email from Heidi Rehm, no redmine.
  • lines changed 2, context: html, text, full: html, text
    c613ca6dd305b556af1148511ecd737317b3fe5b Tue Jun 17 08:48:49 2025 -0700
    improving docs page of deleteriousness supertrack, no redmine, email from Heidi Rehm
  • lines changed 6, context: html, text, full: html, text
    45c657735672d97ab4e9cfd15d4dbe4b056b9066 Tue Jun 17 15:24:32 2025 -0700
    Adding a leading 0 to the ranges. Adding a period after et al., Using HTML entity for double quotes, no Redmine.
  • lines changed 1, context: html, text, full: html, text
    59826a66ca3d544754b5d4292155d2ac384019b3 Tue Jun 17 16:39:58 2025 -0700
    Adding the image of the 'lifted' icon to the text, no Redmine.
  • lines changed 22, context: html, text, full: html, text
    f3ac6bdaf95d5e9a70554ffbff762b1d5229098f Wed Jun 18 16:41:01 2025 -0700
    Updating the revel track from feedback in MLQ #35933
  • lines changed 3, context: html, text, full: html, text
    394790c4392a67d2837427efb96b45038b2d5364 Thu Jun 19 10:07:15 2025 -0700
    Adding a line break and removing the underscore. No RM.
  • lines changed 1, context: html, text, full: html, text
    cbe3d85f5bb91ffbd522c69ec3477c47af157320 Thu Jun 19 10:20:05 2025 -0700
    Needed one more line break.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    9ba17dc870467d703e50e0bab531d590dbbc01ac Tue Jun 17 13:36:36 2025 -0700
    adding another file that I forgot to commit, mea culpa
• src/hg/makeDb/trackDb/maybeBuildHub
  • lines changed 79, context: html, text, full: html, text
    0d7e402cab1ae33138f397deebe5396064a3b43a Wed Jun 18 14:28:34 2025 -0700
    now making hub.txt directly out of the GenArk hub.txt refs #35898
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    386ada600e1f420cacee4b504ede27c63590f098 Thu Jun 19 13:20:14 2025 -0700
    mpxvRivers should be like hs1
• src/hg/makeDb/trackDb/rat/rn8/genArk.trackDb.ra
  • lines changed 594, context: html, text, full: html, text
    96b2dc6c40d4b9b6790fc71a5e217e275695e01f Wed Jun 18 13:58:59 2025 -0700
    initial trackDb from the GenArk hub refs #35898
• src/hg/makeDb/trackDb/zebrafish/danRer12/genArk.trackDb.ra
  • lines changed 249, context: html, text, full: html, text
    fa8c5189bd70f63e4e4570a6abca89ce453f4cc7 Wed Jun 18 15:01:06 2025 -0700
    initial trackDb from GenArk refs #35898
• src/hg/makeDb/trackDb/zebrafish/danRer12/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fa8c5189bd70f63e4e4570a6abca89ce453f4cc7 Wed Jun 18 15:01:06 2025 -0700
    initial trackDb from GenArk refs #35898
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 20, context: html, text, full: html, text
    cc9815dcc544d9bfaa660557feefa1ab4364ecb6 Thu Jun 19 05:45:56 2025 -0700
    add triangles to clinvar tracks, add clinvar lollies to archive, add a validation to the clinvar sub lollies script, refs #35750
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 1, context: html, text, full: html, text
    cc9815dcc544d9bfaa660557feefa1ab4364ecb6 Thu Jun 19 05:45:56 2025 -0700
    add triangles to clinvar tracks, add clinvar lollies to archive, add a validation to the clinvar sub lollies script, refs #35750
• src/hg/utils/otto/clinvar/clinvarSub.sql
  • lines changed 1, context: html, text, full: html, text
    cc9815dcc544d9bfaa660557feefa1ab4364ecb6 Thu Jun 19 05:45:56 2025 -0700
    add triangles to clinvar tracks, add clinvar lollies to archive, add a validation to the clinvar sub lollies script, refs #35750
• src/hg/utils/otto/clinvar/clinvarSubBB.as
  • lines changed 34, context: html, text, full: html, text
    cc9815dcc544d9bfaa660557feefa1ab4364ecb6 Thu Jun 19 05:45:56 2025 -0700
    add triangles to clinvar tracks, add clinvar lollies to archive, add a validation to the clinvar sub lollies script, refs #35750
• src/hg/utils/otto/clinvar/clinvarSubLolly
  • lines changed 17, context: html, text, full: html, text
    cc9815dcc544d9bfaa660557feefa1ab4364ecb6 Thu Jun 19 05:45:56 2025 -0700
    add triangles to clinvar tracks, add clinvar lollies to archive, add a validation to the clinvar sub lollies script, refs #35750
• src/hg/utils/otto/clinvar/clinvarSubLolly.as
  • lines changed 21, context: html, text, full: html, text
    cc9815dcc544d9bfaa660557feefa1ab4364ecb6 Thu Jun 19 05:45:56 2025 -0700
    add triangles to clinvar tracks, add clinvar lollies to archive, add a validation to the clinvar sub lollies script, refs #35750
• src/hg/utils/otto/genArk/pushRR/README.txt
  • lines changed 10, context: html, text, full: html, text
    e8f57e6eaf7d6f0c26290eb27b2c4ee7ca139299 Thu Jun 19 15:14:38 2025 -0700
    moving this cron job from hiram account to otto account refs #34706
  • lines changed 9, context: html, text, full: html, text
    f9a440c2466f991820f1e738522ffb83ad721d60 Fri Jun 20 11:49:03 2025 -0700
    add the Asia node pullHgwdev.sh script refs #34706
• src/hg/utils/otto/genArk/pushRR/alphaBetaPush.pl
  • lines changed 190, context: html, text, full: html, text
    e8f57e6eaf7d6f0c26290eb27b2c4ee7ca139299 Thu Jun 19 15:14:38 2025 -0700
    moving this cron job from hiram account to otto account refs #34706
• src/hg/utils/otto/genArk/pushRR/pullHgwdev.sh
  • lines changed 25, context: html, text, full: html, text
    f9a440c2466f991820f1e738522ffb83ad721d60 Fri Jun 20 11:49:03 2025 -0700
    add the Asia node pullHgwdev.sh script refs #34706
• src/hg/utils/otto/genArk/pushRR/pushRR.sh
  • lines changed 35, context: html, text, full: html, text
    e8f57e6eaf7d6f0c26290eb27b2c4ee7ca139299 Thu Jun 19 15:14:38 2025 -0700
    moving this cron job from hiram account to otto account refs #34706
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    ac62db98d6c7994d55feb2ae1723cd4d2c5c8242 Thu Jun 19 18:28:01 2025 -0700
    Swapping to the new otto script. The Genomics England tracks should be the same display, but now with more items filtered by default due to lax version numbers. The main changes here are the consolidation of multiple scripts into one, and the addition of a panelApp Australia track. Refs #35758
  • lines changed 6, context: html, text, full: html, text
    a8eae8da85b2206130a2510243b814c78ac76df3 Fri Jun 20 11:53:59 2025 -0700
    add the pushRR.sh GenArk script, used to be in Hiram\'s crontab refs #34706
• src/hg/utils/otto/panelApp/doPanelApp.py
  • lines changed 52, context: html, text, full: html, text
    735f7be7f5d6854830d5ef7cc5387fc29027778d Thu Jun 19 18:21:58 2025 -0700
    Making improvements to the panelApp otto job, primarily in support of the new panelApp Australia track. 1. Adding our standard check that will cause an exit if the item count is more than 10% different. 2. Tweak Max's code to fix an issue when specifying the specific panels to extract, this is used for the Australia genes track. 3. Remove the check that only made track items if the versions was >.99, we now make track items out of everything. 4. Max had accidentally specified the two 'onlyPanels' for Genomics England, but it should be Australia. Refs #35758
• src/parasol/paraHub/paraHub.c
  • lines changed 25, context: html, text, full: html, text
    5674b62fd90df90955867e674a8f157a58a0e953 Wed Jun 18 14:33:02 2025 -0700
    Fixes packet overflow issue in Parasol paraNode resurrect. refs #34883
• src/parasol/paraHub/paraHub.h
  • lines changed 1, context: html, text, full: html, text
    5674b62fd90df90955867e674a8f157a58a0e953 Wed Jun 18 14:33:02 2025 -0700
    Fixes packet overflow issue in Parasol paraNode resurrect. refs #34883
• src/parasol/paraNode/paraNode.c
  • lines changed 13, context: html, text, full: html, text
    5674b62fd90df90955867e674a8f157a58a0e953 Wed Jun 18 14:33:02 2025 -0700
    Fixes packet overflow issue in Parasol paraNode resurrect. refs #34883
• src/product/ex.hg.conf
  • lines changed 5, context: html, text, full: html, text
    b4cbd94c19445de87aea4ed3defbaa7c288e78e9 Thu Jun 19 09:50:42 2025 -0700
    Clarifying what is needed to enable the default cart feature. We were missing the hg.conf statement, and also adding the statement to our file of all the possible statements, refs #35862
• src/utils/bigMaxPercDiff/bigMaxPercDiff
  • lines changed 67, context: html, text, full: html, text
    f7212354c8d10da6eaa5ac6618c2428ac7902ccc Thu Jun 19 07:36:50 2025 -0700
    adding a tool bigMaxPercDiff to compare two bigBed/bigWig files and exit with error if they differ in more than x percent, refs #35750
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    f7212354c8d10da6eaa5ac6618c2428ac7902ccc Thu Jun 19 07:36:50 2025 -0700
    adding a tool bigMaxPercDiff to compare two bigBed/bigWig files and exit with error if they differ in more than x percent, refs #35750
• src/utils/qa/check_Tables_Metadata.py
  • lines changed 2, context: html, text, full: html, text
    bb113eaa1fe0e8b96299c8e670b03c2180af94d6 Wed Jun 18 16:40:15 2025 -0700
    Code review edits, refs #35927
• src/utils/qa/hubPublicMail
  • lines changed 2, context: html, text, full: html, text
    44be04dc803317a0d2096d93e5c1cb2d9b2b3c37 Tue Jun 17 15:24:35 2025 -0700
    Update the hubPublicMail script to print the number of failed hubs, No RM
• src/utils/qa/qaTestScript.py
  • lines changed 5, context: html, text, full: html, text
    bb113eaa1fe0e8b96299c8e670b03c2180af94d6 Wed Jun 18 16:40:15 2025 -0700
    Code review edits, refs #35927
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    baf3845f193dfd97a01d070bdfa6f96ee507fe11 Mon Jun 23 23:58:34 2025 -0700
    v484 preview2, refs #35918

• lines changed: 3876
• files changed: 77