All File Changes

v483_preview2 to v483_base (2025-06-02 to 2025-06-09) v483

• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    567584630339484d11ec8312020ccc1702dfb03c Sun Jun 8 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 36, context: html, text, full: html, text
    b960786a48fb9f49ca892ea56a5e742125ab707d Thu Jun 5 11:57:15 2025 -0700
    Adding ADGC6 space for milestones -lab submitted v1 to NIMH last Friday 5/30
  • lines changed 17, context: html, text, full: html, text
    c20816a67291a2cf6f248f8396c73db91a7b6039 Thu Jun 5 12:41:32 2025 -0700
    ADGC6 column[date] row[aim] added ADGC6_E_16 = E/16 in spreadsheet 1_SSPsyGene Milestones RM1MH138309 Kim_FY25_v1 NOTE: they have wrong reporting quarters, expect NIMH v2 will correct
  • lines changed 56, context: html, text, full: html, text
    0994a55f413ccb2180614edc5b7d3fed8928c3c8 Fri Jun 6 11:25:48 2025 -0700
    UCLA new milestones, ADGC1_NO_111213 = column N/O, where O = end-date: 2026Q3(Jul-Sep) thus 2026-10-01 (equiv 2026-09-31) and 111213 refers to rows 11,12,13 per UCLA sspsygene_milestones_yr2_RM1MH132651_JMM_DHG_JMM_V5 excel from NIMH
  • lines changed 50, context: html, text, full: html, text
    4878284d04625dce770834a5819934b485650936 Mon Jun 9 15:12:56 2025 -0700
    Moving Full Text Yale/UCLA milestones to respective AIMs sections
• src/hg/hgHubConnect/hooks/hooklib.c
  • lines changed 54, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 54, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
• src/hg/hgHubConnect/hooks/hooklib.h
  • lines changed 7, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 7, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 27, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 27, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 29, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 29, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 48, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 48, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
  • lines changed 5, context: html, text, full: html, text
    7206132fbc62b1d3b563b67aa067ae8d6ab76e2b Fri Jun 6 15:54:08 2025 -0700
    Refactor hubSpace UI a little in order to make getting the initial filelist over async rather than with the CGI load, refs Max discussion
  • lines changed 1, context: html, text, full: html, text
    29bf34411fc405b99032d38c463528b4361f28da Fri Jun 6 16:14:49 2025 -0700
    Make hubSpace async requests use loginHost cgi-bin url, refs Max discussion
• src/hg/hgPcr/hgPcr.c
  • lines changed 1, context: html, text, full: html, text
    1ee65ce95e96f67f08319b0310f494804453ecfc Mon Jun 9 15:06:40 2025 -0700
    Adding a note that the Target option is only available for human and mouse assemblies, refs #35834
  • lines changed 6, context: html, text, full: html, text
    06f099f6112843f92c8656108372e7194ad96e14 Mon Jun 9 15:20:54 2025 -0700
    Making some of the text on the hgPcr page into a list to reduce the visual clutter, refs #35834
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 18, context: html, text, full: html, text
    c86c38434ba5a31ccafd1ebdabbab00dea55fdc7 Sat Jun 7 11:25:01 2025 -0700
    fix quickLifted bigWig on the negative strand
• src/hg/hgTracks/hgTracks.c
  • lines changed 22, context: html, text, full: html, text
    6670fb5fcdb4479bcfb11971733ad9f9b41b895d Fri Jun 6 12:00:45 2025 -0700
    correct URLs to hgdownload for chrom.sizes.txt and chromAlias.txt files refs #35870
• src/hg/hgTracks/lollyTrack.c
  • lines changed 1, context: html, text, full: html, text
    46ff6457c895cdf0c4f16142414c8f12f692f025 Tue Jun 3 15:27:14 2025 -0700
    fix bug with very small fonts
• src/hg/hgTracks/searchTracks.c
  • lines changed 2, context: html, text, full: html, text
    df74105539e5849345e7b6d6ccc18c4e0295d5f9 Mon Jun 9 14:02:06 2025 -0700
    Fix bug during a refactoring that caused us to try detaching from a thread that was off the end of the thread array. This makes track search on hubs work again, refs #35807
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 5, context: html, text, full: html, text
    96c296bf6fcb45403903e0768b48126c634a83de Tue Jun 3 14:09:56 2025 -0700
    small changes to FAQformat, after call with Brian, no redmine
• src/hg/htdocs/images/encode4LongReadTranscriptsHelp.png
  • lines changed 0, context: html, text, full: html, text
    adf8843854416911d2442c18b26b74fcf0ac0b4b Mon Jun 9 10:43:34 2025 -0700
    Adding example image for encode4 long read transcripts description page
• src/hg/htdocs/indexMeetings.html
  • lines changed 2, context: html, text, full: html, text
    dad92be524cff99d7d0e3c93b19077cbd329f4ea Tue Jun 3 09:30:51 2025 -0700
    Clarifying that the two meetings are full.
  • lines changed 13, context: html, text, full: html, text
    62c2978ae088198633eb0a697f16af5935096b45 Tue Jun 3 11:13:33 2025 -0700
    Adding another workshop.
• src/hg/inc/botDelay.h
  • lines changed 2, context: html, text, full: html, text
    915137728090d52f755d7ad005865871ba4c7209 Mon Jun 2 05:00:54 2025 -0700
    adding file for previous commit
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    c62c78194cfad8453b2d7c74b304fde3ef10b2dc Fri Jun 6 10:46:40 2025 -0700
    Fix missing include bug introduced by 13f391382e54e658, refs browser-qa email
• src/hg/inc/trackDb.h
  • lines changed 2, context: html, text, full: html, text
    f9c9519372b406cf392f199cdd23d1b032fa8e22 Tue Jun 3 12:02:11 2025 -0700
    put quickLifted tracks in the right order and with the right visibilities
• src/hg/inc/userdata.h
  • lines changed 12, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 12, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5979e7af5c783447c2a49ac0c258462fb105d847 Mon Jun 9 21:40:51 2025 -0700
    New version number v483
• src/hg/js/hgMyData.js
  • lines changed 5, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 5, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
  • lines changed 852, context: html, text, full: html, text
    7206132fbc62b1d3b563b67aa067ae8d6ab76e2b Fri Jun 6 15:54:08 2025 -0700
    Refactor hubSpace UI a little in order to make getting the initial filelist over async rather than with the CGI load, refs Max discussion
  • lines changed 5, context: html, text, full: html, text
    29bf34411fc405b99032d38c463528b4361f28da Fri Jun 6 16:14:49 2025 -0700
    Make hubSpace async requests use loginHost cgi-bin url, refs Max discussion
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    22c42295eaa2b41f48a6277e16282c679b3ae05a Tue Jun 3 13:41:51 2025 -0700
    fix horizontal centering for trackDescriptionOnly window in hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    cc6e553cbef4d62c6213aaf1432c67db946c32d8 Tue Jun 3 13:48:43 2025 -0700
    Changing the icon for the track description page right-click option from a wrench to a book, refs #31584
  • lines changed 13, context: html, text, full: html, text
    1504da8476064d2b7cce8c7169d2d88ca1aedbe6 Wed Jun 4 22:22:15 2025 -0700
    QA wants track descriotion on all tracks. tweaking hgTracks.js for right-click menu. refs #31584
• src/hg/js/model/lib/cart.js
  • lines changed 7, context: html, text, full: html, text
    29bf34411fc405b99032d38c463528b4361f28da Fri Jun 6 16:14:49 2025 -0700
    Make hubSpace async requests use loginHost cgi-bin url, refs Max discussion
• src/hg/lib/cart.c
  • lines changed 6, context: html, text, full: html, text
    c91277b19fd78ae350bc9dc6953b56033784fed1 Mon Jun 2 04:59:21 2025 -0700
    bottleneck exception for captcha refs #35824, #35790
  • lines changed 1, context: html, text, full: html, text
    915137728090d52f755d7ad005865871ba4c7209 Mon Jun 2 05:00:54 2025 -0700
    adding file for previous commit
  • lines changed 13, context: html, text, full: html, text
    b89356a235c4592606ec4339b9dc06a6b3fedc1c Thu Jun 5 07:08:26 2025 -0700
    fixing hgGateway captcha problem, at least temporarily, refs #35790
  • lines changed 23, context: html, text, full: html, text
    13f391382e54e6589f383d87069040926c910196 Fri Jun 6 05:57:51 2025 -0700
    fixing web.c to output cookie so hgGateway uses cookies, refs #35824
• src/hg/lib/quickLift.c
  • lines changed 6, context: html, text, full: html, text
    4d4360dde0ef8283aa490ef1a1903dfda56341ab Sat Jun 7 11:28:03 2025 -0700
    fix problems with full elements not being sucked in on negative strand quickLifts
• src/hg/lib/trackHub.c
  • lines changed 77, context: html, text, full: html, text
    f9c9519372b406cf392f199cdd23d1b032fa8e22 Tue Jun 3 12:02:11 2025 -0700
    put quickLifted tracks in the right order and with the right visibilities
  • lines changed 4, context: html, text, full: html, text
    c936950dc182181fc0174ffd5f97d92e2a4c268e Fri Jun 6 16:30:27 2025 -0700
    Updating the hubAssemblyHash == NULL error message, refs #35479
  • lines changed 78, context: html, text, full: html, text
    4a64fe1801134843e9082ab6cea091a5d0eb1c4c Sat Jun 7 11:29:44 2025 -0700
    fix up the list of tracks that will get quickLifted by hgConvert
• src/hg/lib/userdata.c
  • lines changed 109, context: html, text, full: html, text
    b318572799b35ed9cd6fabdeb247495d72d4da4c Tue Jun 3 18:07:28 2025 -0700
    Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058
  • lines changed 109, context: html, text, full: html, text
    134dd0797da608e6b1291f4db6bb5c1033efbfca Thu Jun 5 15:32:25 2025 -0700
    Revert "Make the serverName a required input to hubspace uploads so the hubspace machine can determine where to place uploads. Prevents any current or future username collisions between euro and rr and prevents tusd temp file collisions between the machines, refs #31058" This reverts commit b318572799b35ed9cd6fabdeb247495d72d4da4c.
• src/hg/lib/web.c
  • lines changed 8, context: html, text, full: html, text
    13f391382e54e6589f383d87069040926c910196 Fri Jun 6 05:57:51 2025 -0700
    fixing web.c to output cookie so hgGateway uses cookies, refs #35824
  • lines changed 1, context: html, text, full: html, text
    c62c78194cfad8453b2d7c74b304fde3ef10b2dc Fri Jun 6 10:46:40 2025 -0700
    Fix missing include bug introduced by 13f391382e54e658, refs browser-qa email
• src/hg/logCrawl/trackCounts/README
  • lines changed 11, context: html, text, full: html, text
    26efd8d58625376a6f5f5304697c167db5870dcb Mon Jun 2 14:59:16 2025 -0700
    Adding some missing track counting cronjob scripts to the source tree so qateam can start running them, refs Lou email
• src/hg/logCrawl/trackCounts/makeUsageReport
  • lines changed 375, context: html, text, full: html, text
    26efd8d58625376a6f5f5304697c167db5870dcb Mon Jun 2 14:59:16 2025 -0700
    Adding some missing track counting cronjob scripts to the source tree so qateam can start running them, refs Lou email
• src/hg/logCrawl/trackCounts/runCountByDate.sh
  • lines changed 163, context: html, text, full: html, text
    26efd8d58625376a6f5f5304697c167db5870dcb Mon Jun 2 14:59:16 2025 -0700
    Adding some missing track counting cronjob scripts to the source tree so qateam can start running them, refs Lou email
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 34, context: html, text, full: html, text
    8b26d7af3e7e4915eab698dcc6485ebccc87ddab Mon Jun 2 15:56:23 2025 -0700
    hgdownload2 disk is full send no more data to hgdownload2 refs #35415
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 36, context: html, text, full: html, text
    1f6f906604390fe7ac2dfa3311ea06b0fd99da07 Tue Jun 3 08:25:59 2025 -0700
    adding updated HPRC assemblies refs #35415
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    1d9e6c2f8a07b31b017917eed3893dcb2a7f834b Wed Jun 4 13:36:46 2025 -0700
    adding one per user request refs #29545
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    5ba457463fa459d16abd0588ce7081d7ca2309d9 Wed Jun 4 15:23:09 2025 -0700
    adding one per user request refs #29545
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    8d51a220dccc87d56290b4ec64d14ee196572821 Sat Jun 7 07:42:21 2025 -0700
    adding one per user request refs #29545
  • lines changed 55, context: html, text, full: html, text
    0cdfc4d1a8b9b719096f2f88a7fbc936817e68d3 Sun Jun 8 10:28:01 2025 -0700
    adding updated HPRC assemblies refs #35415
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 2, context: html, text, full: html, text
    1189fc1190d8f1ca86ecb8b51536d68b910c178f Mon Jun 2 15:16:46 2025 -0700
    hgdownload2 disk is full send no more data to hgdownload2 refs #35415
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    1d9e6c2f8a07b31b017917eed3893dcb2a7f834b Wed Jun 4 13:36:46 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 450, context: html, text, full: html, text
    e38f747f95ed21b3081e6ee7a9273e10451c94f3 Mon Jun 9 14:02:17 2025 -0700
    catching up to BRC project list refs #34337
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8d51a220dccc87d56290b4ec64d14ee196572821 Sat Jun 7 07:42:21 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/hg38/clsLongReadRna.txt
  • lines changed 69, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 85, context: html, text, full: html, text
    c116985c1418c05e3d2611a1ccdc8b030b4aeb26 Tue Jun 3 13:46:32 2025 -0700
    moving 77 legacy assemblies to legacy group refs #35415
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 83, context: html, text, full: html, text
    c116985c1418c05e3d2611a1ccdc8b030b4aeb26 Tue Jun 3 13:46:32 2025 -0700
    moving 77 legacy assemblies to legacy group refs #35415
• src/hg/makeDb/doc/mm10.clsLongReadRna.txt
  • lines changed 66, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    5ba457463fa459d16abd0588ce7081d7ca2309d9 Wed Jun 4 15:23:09 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 36, context: html, text, full: html, text
    1f6f906604390fe7ac2dfa3311ea06b0fd99da07 Tue Jun 3 08:25:59 2025 -0700
    adding updated HPRC assemblies refs #35415
  • lines changed 77, context: html, text, full: html, text
    f5c83e11e805bf96fe2dcfd83493e5e27d8b1344 Tue Jun 3 13:18:14 2025 -0700
    moving 77 legacy assemblies to legacy group refs #35415
  • lines changed 55, context: html, text, full: html, text
    0cdfc4d1a8b9b719096f2f88a7fbc936817e68d3 Sun Jun 8 10:28:01 2025 -0700
    adding updated HPRC assemblies refs #35415
• src/hg/makeDb/outside/clsLongReadRna/clsModelBed.as
  • lines changed 19, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/outside/clsLongReadRna/clsTargetBed.as
  • lines changed 12, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/outside/clsLongReadRna/clsTrackTool
  • lines changed 610, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
  • lines changed 1, context: html, text, full: html, text
    7d1fa338ded4783ef25abad8afecfe6ee3077d71 Sat Jun 7 15:03:18 2025 -0700
    keep ordering consistent when clsLongReadRna trackDb is generated
• src/hg/makeDb/outside/clsLongReadRna/gff-attrs-extract.awk
  • lines changed 27, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/trackDb/evaSnp.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    63d2e22e2faf0c23235a743c35b0d52755e455b9 Thu Jun 5 15:58:39 2025 -0700
    Updating the EVA SNP track description page, adding pennantIcon, and adding beta tag, refs #35504
• src/hg/makeDb/trackDb/evaSnpContainer.html
  • lines changed 9, context: html, text, full: html, text
    63d2e22e2faf0c23235a743c35b0d52755e455b9 Thu Jun 5 15:58:39 2025 -0700
    Updating the EVA SNP track description page, adding pennantIcon, and adding beta tag, refs #35504
• src/hg/makeDb/trackDb/human/clinvar.alpha.ra
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    67db2dd6a07c07db8c564893e590ef2e1628fb05 Tue Jun 3 08:25:19 2025 -0700
    adding a label field to the clinvar track, must have a unique name field, refs #35750
• src/hg/makeDb/trackDb/human/genCC.ra
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    92c0acac7717adb611e41616667ee6855bb8fde2 Wed Jun 4 10:19:36 2025 -0700
    Updating genCC mouseover to be clearer, and including the submitter. Refs #35098
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
  • lines changed 82, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.ra
  • lines changed 1075, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
  • lines changed 66, context: html, text, full: html, text
    7d1fa338ded4783ef25abad8afecfe6ee3077d71 Sat Jun 7 15:03:18 2025 -0700
    keep ordering consistent when clsLongReadRna trackDb is generated
• src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.html
  • lines changed 12, context: html, text, full: html, text
    a49ed41de7314fc1dc37588903530fdc3a4c902e Mon Jun 9 10:37:00 2025 -0700
    adding example screenshot to description page for encode4 long read transcripts, refs #31368
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    9095fb95f41797f37fb7d311ce290ca901a2ff96 Tue Jun 3 12:03:10 2025 -0700
    knownGene links need an hgsid for quickLift
• src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.ra
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    abf039ac72dc36c068f70fa890a7ee9cfeb1ab1f Fri Jun 6 16:39:03 2025 -0700
    correcting spelling error in longLabel, refs #35856
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    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    a49ed41de7314fc1dc37588903530fdc3a4c902e Mon Jun 9 10:37:00 2025 -0700
    adding example screenshot to description page for encode4 long read transcripts, refs #31368
• src/hg/makeDb/trackDb/human/trackDb.ra
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    f5108b55dc2ce1a0dacfc261a89523c27440903a Tue Jun 3 12:50:27 2025 -0700
    Adding a track descripiton page for the varaico track to describe the colors for the track, refs #34595
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    cf8e313fa049cdeb9f3c2116a204727144625478 Mon Jun 9 09:45:31 2025 -0700
    Adding predictionScoresSuper.ra to human/trackDb.ra due to it being moved, refs #27766
• src/hg/makeDb/trackDb/human/varaico.html
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    f5108b55dc2ce1a0dacfc261a89523c27440903a Tue Jun 3 12:50:27 2025 -0700
    Adding a track descripiton page for the varaico track to describe the colors for the track, refs #34595
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
  • lines changed 82, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra
  • lines changed 911, context: html, text, full: html, text
    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
  • lines changed 61, context: html, text, full: html, text
    7d1fa338ded4783ef25abad8afecfe6ee3077d71 Sat Jun 7 15:03:18 2025 -0700
    keep ordering consistent when clsLongReadRna trackDb is generated
• src/hg/makeDb/trackDb/mouse/mm10/encode4LongRnaTranscripts.html
  • lines changed 11, context: html, text, full: html, text
    a49ed41de7314fc1dc37588903530fdc3a4c902e Mon Jun 9 10:37:00 2025 -0700
    adding example screenshot to description page for encode4 long read transcripts, refs #31368
• src/hg/makeDb/trackDb/mouse/mm10/long_read_transcripts.ra
  • lines changed 1, context: html, text, full: html, text
    abf039ac72dc36c068f70fa890a7ee9cfeb1ab1f Fri Jun 6 16:39:03 2025 -0700
    correcting spelling error in longLabel, refs #35856
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    2373cd564a862f870831fc66bb4687e422848ffa Sat Jun 7 14:11:06 2025 -0700
    Import of CLS Long Read Data from GENCODE / CRG (aka what I did in Barcelona)
  • lines changed 1, context: html, text, full: html, text
    6a868b2979406dfe606080a096c938c6bc1963a0 Sat Jun 7 15:02:28 2025 -0700
    fixed stray character that failed to create super track
• src/hg/makeDb/trackDb/tagTypes.tab
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    232caa279c443ef97078067b4b27cdac12e4eca7 Tue Jun 3 12:43:41 2025 -0700
    allow bigGenePred to use hgsid
• src/hg/makeDb/trackDb/trackDb.ra
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    63d2e22e2faf0c23235a743c35b0d52755e455b9 Thu Jun 5 15:58:39 2025 -0700
    Updating the EVA SNP track description page, adding pennantIcon, and adding beta tag, refs #35504
• src/inc/srcVersion.h
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    5979e7af5c783447c2a49ac0c258462fb105d847 Mon Jun 9 21:40:51 2025 -0700
    New version number v483
• src/product/ex.hg.conf
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    293f56b870f9fb706cde5cc427e074a7c6d664b6 Tue Jun 3 11:27:59 2025 -0700
    Doc'ing 3 missing hg.conf settings, refs #33812
• src/utils/qa/hgTracksTiming.py
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    62c58443da3f62b5ac33c1933e6abc3b249b2ba0 Tue Jun 3 15:31:31 2025 -0700
    Updating hgTracksTiming for two purposes: 1. Making it take command-line arguments so what we can call it separately for the development machines vs. live servers. The reason for this is that we don't need to spam the genome-alert ML for hgwbeta or dev issues. 2. It was previously writing out very low response times that came from failures like the captcha or not finding hgTracks end to the log file. This was throwing off the usage numbers as low values are good, but in this case they are errors. No RM.
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    a5f3fff630cd9743abf97b1984c0b9869eb85cfc Wed Jun 4 07:58:10 2025 -0700
    Wrapping the request function in a try statement so that when the server is entirely unresponsive we don't get a spam requests lib spam, but instead get a two line email about the issue. No RM.
• src/utils/qa/trackCountsParse
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    cfa9546a9f8fe1b79434faa7ec9cf81093b57d34 Tue Jun 3 13:43:30 2025 -0700
    Some small tweaks to the trackCountsParse script that generates a list of potential tracks to nest or hide based on usage. 1. Check to see if the makeUsageReport script has ran, and if not run it for those dates. 2. Cleaned up some greps that needed escaped backslashes. 3. Typo fix. 4. Clarifying the line to call an easy to format tabFmt script. Refs #35858
• src/utils/qa/weeklybld/buildEnv.csh
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    93801ca2fd1c6cc83c2591ea7f9987d75be7abe2 Mon Jun 9 21:40:25 2025 -0700
    v483 final build, refs #35819

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