All File Changes

v477_base to v478_preview (2025-02-03 to 2025-02-10) v478

• confs/hgwbeta.hg.conf
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    53b21444c44530593b37529acb63d2a74f7f4f28 Sun Feb 9 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 9, context: html, text, full: html, text
    53b21444c44530593b37529acb63d2a74f7f4f28 Sun Feb 9 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/changes.txt
  • lines changed 4, context: html, text, full: html, text
    a496e0870b71996706451925c8833d48e6d7a49a Thu Feb 6 10:51:34 2025 -0800
    Pausing GBiB CGI updates until we can get Rocky-compiled CGIs working there, refs #35183
  • lines changed 2, context: html, text, full: html, text
    60d33ad712a93a9c66a3d89fa8126d4938603eb4 Thu Feb 6 12:24:41 2025 -0800
    And updating the browserbox changes doc, refs #35183
• src/browserbox/root/updateBrowser.sh
  • lines changed 4, context: html, text, full: html, text
    a496e0870b71996706451925c8833d48e6d7a49a Thu Feb 6 10:51:34 2025 -0800
    Pausing GBiB CGI updates until we can get Rocky-compiled CGIs working there, refs #35183
  • lines changed 5, context: html, text, full: html, text
    1f1580e080a70d06a0330a5693d47e1c3bcac077 Thu Feb 6 12:23:16 2025 -0800
    New plan, letting GBiB update as normal but from a frozen set of binaries for now. refs #35183
• src/hg/cgilib/makefile
  • lines changed 2, context: html, text, full: html, text
    37d8f22d578c0cb7ed85aea230424db6eb22585e Wed Feb 5 12:41:16 2025 -0800
    mv cartTrackDb.c and wikiTrack.c into hg/lib
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 2, context: html, text, full: html, text
    ca4aae23b28a84c5c661a24f588c3a004f192cff Mon Feb 3 15:37:07 2025 -0800
    Updating status in Timeline, done=grey, per last DRACC meeting with Catharina
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 5, context: html, text, full: html, text
    c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f Mon Feb 3 17:36:09 2025 -0800
    Revert "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit 156dbcfc96c9a4a5eba481f8d979700b0ca1024e.
  • lines changed 5, context: html, text, full: html, text
    f20e513a5dcae8e821aaf7dcccfaf57ee4cd3cb1 Thu Feb 6 13:37:43 2025 -0800
    Reapply "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f.
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    e97696bf0ffbe83d71bf11befb14a46b9134b245 Thu Feb 6 11:19:25 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
  • lines changed 12, context: html, text, full: html, text
    ea1bd03c5da8c0e084bbf39e938c25760167b03f Thu Feb 6 11:48:24 2025 -0800
    had the logic backwards on that isCuratedHubUrl function refs #34706
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
• src/hg/hgHubConnect/hgHubConnect.h
  • lines changed 5, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 1, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
• src/hg/hgHubConnect/makefile
  • lines changed 4, context: html, text, full: html, text
    b54bfb0c87c9d8f806d86a15d447089ed073b32e Mon Feb 10 09:33:08 2025 -0800
    Only make tusd hooks when on hgwdev, refs Michael Hiller email
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 24, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 3, context: html, text, full: html, text
    aa1e818e2d2bd577194b0cdda7d561b93b948553 Mon Feb 3 16:38:55 2025 -0800
    Check that the current db is the same as org before setting ctDb to it.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 2, context: html, text, full: html, text
    a84136501e80887728062e36eca4c09b0a1c222f Mon Feb 3 16:35:56 2025 -0800
    Fix corner case uninitialized variable, thx Marc Perry.
• src/hg/hgTracks/bedTrack.c
  • lines changed 45, context: html, text, full: html, text
    0b9c2a6f9930555f65104385a9edcb00147a5bc6 Mon Feb 3 09:31:56 2025 -0800
    add support for quikLifting mySQL beds.
  • lines changed 18, context: html, text, full: html, text
    49f31ee05d781083f1a9b7fcff2e99b974622c41 Tue Feb 4 09:06:51 2025 -0800
    add custom tracks
  • lines changed 2, context: html, text, full: html, text
    11bc4be74936249529960fb3a532376779debbe5 Thu Feb 6 11:06:45 2025 -0800
    add hgc support for click throughs on quickLifted custom tracks
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    49f31ee05d781083f1a9b7fcff2e99b974622c41 Tue Feb 4 09:06:51 2025 -0800
    add custom tracks
• src/hg/hgc/hgc.c
  • lines changed 36, context: html, text, full: html, text
    7f8b631eb54a42bd40d48dcdd85103cbc97ae534 Tue Feb 4 09:59:00 2025 -0800
    pull out table named based handling into a separate function that can be avoided if desired.
  • lines changed 4, context: html, text, full: html, text
    1c7d36e357be58d14a6bc36bb1438f44743cfb08 Wed Feb 5 09:09:23 2025 -0800
    fix problem with hgc complaining about the click not doing anything
  • lines changed 40, context: html, text, full: html, text
    11bc4be74936249529960fb3a532376779debbe5 Thu Feb 6 11:06:45 2025 -0800
    add hgc support for click throughs on quickLifted custom tracks
• src/hg/hgc/peakClusters.c
  • lines changed 18, context: html, text, full: html, text
    7df3ba2728fb2b20ac6159bb4935b9ccd829e695 Thu Feb 6 13:31:32 2025 -0800
    squashed hgEncodeVocab-ra-danger-fix. fixes #287
• src/hg/htdocs/goldenPath/help/net.html
  • lines changed 1, context: html, text, full: html, text
    c342217f25d2ac60b96871d4260794c0c248bf16 Wed Feb 5 13:45:53 2025 -0800
    minor correction from code review, refs #35151
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 7, context: html, text, full: html, text
    2dda0948f6bab888270b20a00885371310c52230 Wed Feb 5 06:46:10 2025 -0800
    docing highlightValues, refs #33692
• src/hg/htdocs/style/hgMyData.css
  • lines changed 11, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    20b86eabfde1a98c55bcc787d287d8c53741422c Thu Feb 6 11:20:30 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f Mon Feb 3 17:36:09 2025 -0800
    Revert "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit 156dbcfc96c9a4a5eba481f8d979700b0ca1024e.
  • lines changed 1, context: html, text, full: html, text
    f20e513a5dcae8e821aaf7dcccfaf57ee4cd3cb1 Thu Feb 6 13:37:43 2025 -0800
    Reapply "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f.
• src/hg/inc/quickLift.h
  • lines changed 6, context: html, text, full: html, text
    0b9c2a6f9930555f65104385a9edcb00147a5bc6 Mon Feb 3 09:31:56 2025 -0800
    add support for quikLifting mySQL beds.
  • lines changed 5, context: html, text, full: html, text
    11bc4be74936249529960fb3a532376779debbe5 Thu Feb 6 11:06:45 2025 -0800
    add hgc support for click throughs on quickLifted custom tracks
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    e97696bf0ffbe83d71bf11befb14a46b9134b245 Thu Feb 6 11:19:25 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
• src/hg/js/hgMyData.js
  • lines changed 273, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
  • lines changed 3, context: html, text, full: html, text
    4eaa725ec7a9382204f5be71be134286f2fdad98 Fri Feb 7 15:01:13 2025 -0800
    Allow spaces in hub names on hubspace client
• src/hg/lib/cartTrackDb.c
  • lines changed 0, context: html, text, full: html, text
    37d8f22d578c0cb7ed85aea230424db6eb22585e Wed Feb 5 12:41:16 2025 -0800
    mv cartTrackDb.c and wikiTrack.c into hg/lib
• src/hg/lib/cv.c
  • lines changed 1, context: html, text, full: html, text
    c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f Mon Feb 3 17:36:09 2025 -0800
    Revert "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit 156dbcfc96c9a4a5eba481f8d979700b0ca1024e.
  • lines changed 1, context: html, text, full: html, text
    f20e513a5dcae8e821aaf7dcccfaf57ee4cd3cb1 Thu Feb 6 13:37:43 2025 -0800
    Reapply "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f.
• src/hg/lib/hdb.c
  • lines changed 17, context: html, text, full: html, text
    20b86eabfde1a98c55bcc787d287d8c53741422c Thu Feb 6 11:20:30 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
  • lines changed 3, context: html, text, full: html, text
    ea1bd03c5da8c0e084bbf39e938c25760167b03f Thu Feb 6 11:48:24 2025 -0800
    had the logic backwards on that isCuratedHubUrl function refs #34706
  • lines changed 5, context: html, text, full: html, text
    6a354f679c0fd5ed0ab5b4feae6d400691ad28e2 Thu Feb 6 12:10:28 2025 -0800
    this is crazy upside down logic . . . refs #34706
• src/hg/lib/hubConnect.c
  • lines changed 4, context: html, text, full: html, text
    0b9c2a6f9930555f65104385a9edcb00147a5bc6 Mon Feb 3 09:31:56 2025 -0800
    add support for quikLifting mySQL beds.
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f Mon Feb 3 17:36:09 2025 -0800
    Revert "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit 156dbcfc96c9a4a5eba481f8d979700b0ca1024e.
  • lines changed 0, context: html, text, full: html, text
    7df3ba2728fb2b20ac6159bb4935b9ccd829e695 Thu Feb 6 13:31:32 2025 -0800
    squashed hgEncodeVocab-ra-danger-fix. fixes #287
  • lines changed 16, context: html, text, full: html, text
    f20e513a5dcae8e821aaf7dcccfaf57ee4cd3cb1 Thu Feb 6 13:37:43 2025 -0800
    Reapply "Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting." This reverts commit c5af95b7146dde46f2d2f70ecad1eb9b4c37b57f.
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    37d8f22d578c0cb7ed85aea230424db6eb22585e Wed Feb 5 12:41:16 2025 -0800
    mv cartTrackDb.c and wikiTrack.c into hg/lib
• src/hg/lib/quickLift.c
  • lines changed 94, context: html, text, full: html, text
    0b9c2a6f9930555f65104385a9edcb00147a5bc6 Mon Feb 3 09:31:56 2025 -0800
    add support for quikLifting mySQL beds.
  • lines changed 2, context: html, text, full: html, text
    11bc4be74936249529960fb3a532376779debbe5 Thu Feb 6 11:06:45 2025 -0800
    add hgc support for click throughs on quickLifted custom tracks
• src/hg/lib/trackHub.c
  • lines changed 8, context: html, text, full: html, text
    0b9c2a6f9930555f65104385a9edcb00147a5bc6 Mon Feb 3 09:31:56 2025 -0800
    add support for quikLifting mySQL beds.
  • lines changed 26, context: html, text, full: html, text
    49f31ee05d781083f1a9b7fcff2e99b974622c41 Tue Feb 4 09:06:51 2025 -0800
    add custom tracks
  • lines changed 11, context: html, text, full: html, text
    11bc4be74936249529960fb3a532376779debbe5 Thu Feb 6 11:06:45 2025 -0800
    add hgc support for click throughs on quickLifted custom tracks
• src/hg/lib/userdata.c
  • lines changed 1, context: html, text, full: html, text
    cd0b41f1116bd93328ab34e9eceaa5f9afa8b825 Thu Feb 6 13:36:29 2025 -0800
    Lots of changes to hub space UI after code review and QA feedback. 1) Make the table interface more like a file explorer where you view the 'root' directory by default and then can click into 'folders'. Also adds a breadcrumb nav so you can go backwards. 2) Fix bug in delete command to remove directories correctly. 3) cgiEncode the parentDir of incoming requests to prevent moving files to weird locations
• src/hg/lib/wikiTrack.c
  • lines changed 0, context: html, text, full: html, text
    37d8f22d578c0cb7ed85aea230424db6eb22585e Wed Feb 5 12:41:16 2025 -0800
    mv cartTrackDb.c and wikiTrack.c into hg/lib
• src/hg/logCrawl/trimLogs/runTrimLogs.sh
  • lines changed 13, context: html, text, full: html, text
    9461632185d991b472fb061651d21c358c5690ba Mon Feb 10 10:52:53 2025 -0800
    Make track log trim script use hgwdev as a cluster instead of ku, refs Lou email
• src/hg/makeDb/doc/asmHubs/findEquiv.py
  • lines changed 150, context: html, text, full: html, text
    a4bf3820f12a2275c02f005c60fd84f56df26c09 Tue Feb 4 13:34:48 2025 -0800
    find GenArk equivalents given a list of accessions for Tiberius (and other data) import refs #34917
  • lines changed 3, context: html, text, full: html, text
    47ca1286ce276827df0a092c5bf3be1fbfabe1ee Tue Feb 4 13:43:03 2025 -0800
    output list in sorted order refs #34917
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    49a135dcc0b53ceb23131551d47e9417fed3ac95 Mon Feb 3 17:43:20 2025 -0800
    adding 1 per user request and updating one RefSeq refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    49a135dcc0b53ceb23131551d47e9417fed3ac95 Mon Feb 3 17:43:20 2025 -0800
    adding 1 per user request and updating one RefSeq refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    49a135dcc0b53ceb23131551d47e9417fed3ac95 Mon Feb 3 17:43:20 2025 -0800
    adding 1 per user request and updating one RefSeq refs #29545
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 43, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/doc/hg19.txt
  • lines changed 20, context: html, text, full: html, text
    e9cbd875e607d5774dfbc19ff8c389ff9ec851f6 Thu Feb 6 12:09:35 2025 -0800
    make quickLift chain from hg19 to hg38
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 44, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/doc/hg38/splicevardb.txt
  • lines changed 0, context: html, text, full: html, text
    8275cd0d4c6758f9d602d1e3c54c809274dfdd00 Wed Feb 5 06:16:50 2025 -0800
    moving track docs, refs #34424
  • lines changed 3, context: html, text, full: html, text
    251dfb34e6bd663206ffcd3e971658b787400266 Wed Feb 5 06:35:26 2025 -0800
    fixing typos in makedoc, refs #34424
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 45, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/hgGoldGapGl/makefile
  • lines changed 1, context: html, text, full: html, text
    a9bc64a2b2176fb78f9270dc7b5bbe1022be9b8b Mon Feb 10 10:43:16 2025 -0800
    Correcting presumed typo, refs #35179
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 8, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 277, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/chimp/panTro2/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/cow/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/alphaMissense.html
  • lines changed 18, context: html, text, full: html, text
    ee6aa4821b235509fa6827f7a7b29abe0f3a4862 Mon Feb 10 08:42:39 2025 -0800
    minor tweaks to AlphaMissense description page, refs #32269
• src/hg/makeDb/trackDb/human/hg17/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 14, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.html
  • lines changed 32, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra
  • lines changed 210, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 8, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.html
  • lines changed 47, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra
  • lines changed 247, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/human/hs1/dbSNP155.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html
  • lines changed 3, context: html, text, full: html, text
    97acea61b7566425b79b11b95e767ac35d693cbe Wed Feb 5 10:34:41 2025 -0800
    Fixing a typo. Missina 'a' in 'comparative', no Redmine.
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 5, context: html, text, full: html, text
    0600b1ca44df66fa059b55f2357c0df6387d64b5 Thu Feb 6 12:03:54 2025 -0800
    Turning SpliceAI into a composite instead of a superTrack so it can be nested in the splicing impact track, refs #34823
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
  • lines changed 29, context: html, text, full: html, text
    64bd5703470f683544d89164884fe40ec30b71bc Thu Feb 6 16:45:59 2025 -0800
    Added more details to spliceImpactSuper.html and added a SpliceVarDB link on the hgc page, refs #34424
• src/hg/makeDb/trackDb/human/splicevardb.ra
  • lines changed 4, context: html, text, full: html, text
    64bd5703470f683544d89164884fe40ec30b71bc Thu Feb 6 16:45:59 2025 -0800
    Added more details to spliceImpactSuper.html and added a SpliceVarDB link on the hgc page, refs #34424
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
  • lines changed 1, context: html, text, full: html, text
    00efacf7cf16ff0043d37397c51ab147b72e1b6b Fri Feb 7 13:42:55 2025 -0800
    Adding version to varChat track, refs #35081
• src/hg/makeDb/trackDb/mouse/mm10/dbSnpArchiveMm10.ra
  • lines changed 3, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.html
  • lines changed 30, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra
  • lines changed 247, context: html, text, full: html, text
    8debce5b56bcc570ddff4226bf9b04c30e4f6f29 Wed Feb 5 12:48:04 2025 -0800
    import of GENCODE Versions VM37, V48, V48lift37
• src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/rat/rn4/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c9d07faded9290f07ac59bd3a52aaa4563ee974f Wed Feb 5 14:17:06 2025 -0800
    Adding tableBrowser noGenome to All SNPs tracks, #29953
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 6, context: html, text, full: html, text
    60273bfc304c4c57c18aa443f6fe6f96705058f9 Mon Feb 3 15:13:20 2025 -0800
    should be passing along the gff3 file to download directory - get the symLinked file here refs #35027
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 1, context: html, text, full: html, text
    08860b2a6b9377fd7deece38f70c17ae73455a64 Mon Feb 3 14:46:13 2025 -0800
    should be passing along the gff3 file to download directory - get the symLinked file here refs #35027
  • lines changed 4, context: html, text, full: html, text
    e603c24b1c5f12d0fdb9c3d8b85d93cc54599921 Mon Feb 3 15:10:57 2025 -0800
    better to make a gtf for ncbiGene like all the others refs #35027
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 75, context: html, text, full: html, text
    8d7fca788984ae4f0dde81e775574cc24bd58bbf Mon Feb 3 14:00:13 2025 -0800
    updated to new window masker binary and now bash scripts in place of the C-shell scripts no redmine
• src/hg/utils/otto/otto.crontab
  • lines changed 3, context: html, text, full: html, text
    5253452667b95976d5b2f10a20d2b509306f4406 Fri Feb 7 13:45:49 2025 -0800
    Adding VarChat track to otto, refs #35197
• src/hg/utils/otto/varChat/varChatOtto.sh
  • lines changed 52, context: html, text, full: html, text
    5253452667b95976d5b2f10a20d2b509306f4406 Fri Feb 7 13:45:49 2025 -0800
    Adding VarChat track to otto, refs #35197
• src/utils/qa/weeklybld/buildEnv.csh
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    a0d77a4002927edc5847477856e8bd1c1375b973 Mon Feb 10 10:57:34 2025 -0800
    v478 preview1, refs #35106
• src/utils/qa/weeklybld/cherryPickCommits.csh
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    acdaa07de466a99a62b4ed7d026d4adb89893584 Mon Feb 3 19:51:05 2025 -0800
    Seems like -t is no longer accepted as meaning --track=direct by git, so being explicit. No ticket.
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 1, context: html, text, full: html, text
    acdaa07de466a99a62b4ed7d026d4adb89893584 Mon Feb 3 19:51:05 2025 -0800
    Seems like -t is no longer accepted as meaning --track=direct by git, so being explicit. No ticket.
• src/utils/qa/weeklybld/doJavaUtilBuild.csh
  • lines changed 1, context: html, text, full: html, text
    a361791ca98af0188613d52ac64b0168ff25f519 Mon Feb 3 19:55:02 2025 -0800
    A few more places where git wants explicit --track=direct, no ticket
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 1, context: html, text, full: html, text
    a361791ca98af0188613d52ac64b0168ff25f519 Mon Feb 3 19:55:02 2025 -0800
    A few more places where git wants explicit --track=direct, no ticket
• src/utils/qa/weeklybld/revertCommits.csh
  • lines changed 2, context: html, text, full: html, text
    a361791ca98af0188613d52ac64b0168ff25f519 Mon Feb 3 19:55:02 2025 -0800
    A few more places where git wants explicit --track=direct, no ticket
• src/utils/qa/weeklybld/sendLogEmail.pl
  • lines changed 1, context: html, text, full: html, text
    2757f15a9285e4d56bedf7d1004991aebe1b46f7 Mon Feb 3 20:46:04 2025 -0800
    s-nail wants spaces instead of commas in the recipient list, no ticket

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• files changed: 119