All File Changes

v475_base to v476_preview (2024-12-09 to 2024-12-16) v476

• src/hg/hgBeacon/hgBeacon
  • lines changed 24, context: html, text, full: html, text
    84b876bd80b78018f4f71360a464c43dfe699431 Thu Dec 12 02:45:06 2024 -0800
    porting hgBeacon to python3, refs #34921
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    03def7ecdfe20de5dfd39cdf5a4410d0a0e72949 Wed Dec 4 15:56:05 2024 -0800
    Updating the keyboard shortcut text for the Multi-Region pop-up menu, refs #18752
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 65, context: html, text, full: html, text
    9af4842cd888f9150257834edb17991f7a2ae697 Mon Dec 9 11:49:34 2024 -0800
    Added a FAQ entry for SuperTracks vs composite tracks, refs #28196
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 34, context: html, text, full: html, text
    b63002965b8608c38af0c85ede421e7e79bd8d0d Wed Dec 11 11:53:28 2024 -0800
    Announcing the DDG2P track, refs #34097
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    b63002965b8608c38af0c85ede421e7e79bd8d0d Wed Dec 11 11:53:28 2024 -0800
    Announcing the DDG2P track, refs #34097
• src/hg/js/ajax.js
  • lines changed 2, context: html, text, full: html, text
    a784cf4f2f57d30f1b1f789075e1bc07d1a0ad45 Wed Dec 11 06:53:44 2024 -0800
    fixing 32k cart string limit on Safari and Edge, refs #34911
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    3f68f3064052f4ed11651f954ee121282456ab1f Thu Dec 12 03:05:56 2024 -0800
    fix after code review, refs #34936
  • lines changed 4, context: html, text, full: html, text
    853d8038a5874ee0c8ba45b7584134f4deadb312 Mon Dec 16 03:31:39 2024 -0800
    first step towards a solution for the all children hidden problem, refs #34959
• src/hg/js/utils.js
  • lines changed 48, context: html, text, full: html, text
    8fa873a8a5051f55f7d6f6473e438b314e0c4bc1 Mon Dec 16 07:57:12 2024 -0800
    trying to improve the hide tracks function again, refs #34959
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    0f2d61eb03ad97b5b8f151317f3b065733a891ff Wed Dec 11 10:16:10 2024 -0800
    adding one per user request refs #29545
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 17, context: html, text, full: html, text
    0104796f18e0ee85ccaa6f76caeacb055a42bc6c Mon Dec 9 12:09:08 2024 -0800
    keep dynaBlat/backUpLinks hierarchy up to date refs #33526
  • lines changed 57, context: html, text, full: html, text
    7580b50c5626bfbd3d6f90c7fb45dd899e335c64 Mon Dec 9 13:00:46 2024 -0800
    now staging everything on /gbdb/genark/ some redmine reference
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    9e65e54f0f956ea44785df0427f0f457fcfbb34c Fri Dec 13 05:34:09 2024 -0800
    fix for hg19 revel track, refs #34947
• src/hg/makeDb/doc/hg38/cadd.txt
  • lines changed 3, context: html, text, full: html, text
    9d56da4ed4b38921527ecb425c79f7f809408345 Fri Dec 13 14:08:41 2024 -0800
    Adding colors to the REVEL and CADD tracks, refs #34732
• src/hg/makeDb/doc/hg38/revel.txt
  • lines changed 4, context: html, text, full: html, text
    9e65e54f0f956ea44785df0427f0f457fcfbb34c Fri Dec 13 05:34:09 2024 -0800
    fix for hg19 revel track, refs #34947
  • lines changed 3, context: html, text, full: html, text
    9d56da4ed4b38921527ecb425c79f7f809408345 Fri Dec 13 14:08:41 2024 -0800
    Adding colors to the REVEL and CADD tracks, refs #34732
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    0f2d61eb03ad97b5b8f151317f3b065733a891ff Wed Dec 11 10:16:10 2024 -0800
    adding one per user request refs #29545
• src/hg/makeDb/doc/ncbiRefSeq/ncbiOrtho.makedoc
  • lines changed 89, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/doc/ncbiRefSeq/ortho.py
  • lines changed 207, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 70, context: html, text, full: html, text
    366ce67b8b7f69df2eaab2db4747f1437842f6fb Thu Dec 12 11:04:37 2024 -0800
    update common names refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 138, context: html, text, full: html, text
    366ce67b8b7f69df2eaab2db4747f1437842f6fb Thu Dec 12 11:04:37 2024 -0800
    update common names refs #34370
• src/hg/makeDb/revel/revel.as
  • lines changed 1, context: html, text, full: html, text
    9e65e54f0f956ea44785df0427f0f457fcfbb34c Fri Dec 13 05:34:09 2024 -0800
    fix for hg19 revel track, refs #34947
  • lines changed 2, context: html, text, full: html, text
    d642cf5039fe119b031d57590a4d9644bf9d90fa Mon Dec 16 05:49:18 2024 -0800
    bed9 fix for revel overlap track, due to my oversight in previous commit, refs #34947
• src/hg/makeDb/revel/revelToWig-hg19.py
  • lines changed 122, context: html, text, full: html, text
    9e65e54f0f956ea44785df0427f0f457fcfbb34c Fri Dec 13 05:34:09 2024 -0800
    fix for hg19 revel track, refs #34947
• src/hg/makeDb/revel/revelToWig-hg38.py
  • lines changed 146, context: html, text, full: html, text
    9e65e54f0f956ea44785df0427f0f457fcfbb34c Fri Dec 13 05:34:09 2024 -0800
    fix for hg19 revel track, refs #34947
• src/hg/makeDb/revel/revelToWig.py
  • lines changed 187, context: html, text, full: html, text
    9e65e54f0f956ea44785df0427f0f457fcfbb34c Fri Dec 13 05:34:09 2024 -0800
    fix for hg19 revel track, refs #34947
  • lines changed 1, context: html, text, full: html, text
    d642cf5039fe119b031d57590a4d9644bf9d90fa Mon Dec 16 05:49:18 2024 -0800
    bed9 fix for revel overlap track, due to my oversight in previous commit, refs #34947
• src/hg/makeDb/trackDb/human/cadd1_7.ra
  • lines changed 4, context: html, text, full: html, text
    9d56da4ed4b38921527ecb425c79f7f809408345 Fri Dec 13 14:08:41 2024 -0800
    Adding colors to the REVEL and CADD tracks, refs #34732
• src/hg/makeDb/trackDb/human/caddSuper1_7.html
  • lines changed 29, context: html, text, full: html, text
    9d56da4ed4b38921527ecb425c79f7f809408345 Fri Dec 13 14:08:41 2024 -0800
    Adding colors to the REVEL and CADD tracks, refs #34732
• src/hg/makeDb/trackDb/human/civic.ra
  • lines changed 2, context: html, text, full: html, text
    cbfe2c0af6949ffd02b9f52f5734d2d44c3c9011 Thu Dec 12 14:26:34 2024 -0800
    CIViC: add mouseover text and full otto crontab refs #34371
• src/hg/makeDb/trackDb/human/decipher.alpha.ra
  • lines changed 5, context: html, text, full: html, text
    b63002965b8608c38af0c85ede421e7e79bd8d0d Wed Dec 11 11:53:28 2024 -0800
    Announcing the DDG2P track, refs #34097
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 35, context: html, text, full: html, text
    bfc63f827fd1e5eff262fadfc9afdca7335c9216 Wed Dec 11 13:48:25 2024 -0800
    Releasing the DDG2P track to the RR, refs #34097
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
  • lines changed 10, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 26, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 2, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 2, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 2, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 2, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 2, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    4198b98cde5df825c17b1e312b65e33d4c27aebd Tue Dec 10 05:42:51 2024 -0800
    renaming conservation tracks, refs #34909
  • lines changed 7, context: html, text, full: html, text
    cbfe2c0af6949ffd02b9f52f5734d2d44c3c9011 Thu Dec 12 14:26:34 2024 -0800
    CIViC: add mouseover text and full otto crontab refs #34371
• src/hg/makeDb/trackDb/human/refSeqComposite.html
  • lines changed 34, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/trackDb/human/revel.html
  • lines changed 27, context: html, text, full: html, text
    9d56da4ed4b38921527ecb425c79f7f809408345 Fri Dec 13 14:08:41 2024 -0800
    Adding colors to the REVEL and CADD tracks, refs #34732
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 16, context: html, text, full: html, text
    1b05a306aedcea99e18dfa34fadccfdf67e295b7 Tue Dec 10 10:46:07 2024 -0800
    Updated the mouseOverField and removed the release tags, refs #34931
  • lines changed 4, context: html, text, full: html, text
    9d56da4ed4b38921527ecb425c79f7f809408345 Fri Dec 13 14:08:41 2024 -0800
    Adding colors to the REVEL and CADD tracks, refs #34732
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    bfc63f827fd1e5eff262fadfc9afdca7335c9216 Wed Dec 11 13:48:25 2024 -0800
    Releasing the DDG2P track to the RR, refs #34097
  • lines changed 1, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/trackDb/mouse/mm39/refSeqComposite.html
  • lines changed 30, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
  • lines changed 20, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 30, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 20, context: html, text, full: html, text
    a919a3dbe5fd770f03b4c879612b123e04743a9c Thu Dec 12 23:47:12 2024 -0800
    Adding the Gene Orthologs track to the NCBI RefSeq composite track, refs #30262
• src/hg/utils/automation/doRepeatModeler.pl
  • lines changed 4, context: html, text, full: html, text
    a1790e2b1d8c1d197bb1348554322a783a9b2adf Thu Dec 12 13:49:09 2024 -0800
    this process really wants to be on /dev/shm/ before /scratch/tmp/ refs #34370
• src/hg/utils/otto/civic/civic.as
  • lines changed 1, context: html, text, full: html, text
    cbfe2c0af6949ffd02b9f52f5734d2d44c3c9011 Thu Dec 12 14:26:34 2024 -0800
    CIViC: add mouseover text and full otto crontab refs #34371
• src/hg/utils/otto/civic/civicToBed.py
  • lines changed 69, context: html, text, full: html, text
    cbfe2c0af6949ffd02b9f52f5734d2d44c3c9011 Thu Dec 12 14:26:34 2024 -0800
    CIViC: add mouseover text and full otto crontab refs #34371
• src/hg/utils/otto/civic/doCivicUpdate.sh
  • lines changed 9, context: html, text, full: html, text
    cbfe2c0af6949ffd02b9f52f5734d2d44c3c9011 Thu Dec 12 14:26:34 2024 -0800
    CIViC: add mouseover text and full otto crontab refs #34371
• src/hg/utils/otto/otto.crontab
  • lines changed 4, context: html, text, full: html, text
    cbfe2c0af6949ffd02b9f52f5734d2d44c3c9011 Thu Dec 12 14:26:34 2024 -0800
    CIViC: add mouseover text and full otto crontab refs #34371
• src/inc/common.mk
  • lines changed 42, context: html, text, full: html, text
    e2a6d11349d8404362291dd6d644c701e871f1f9 Thu Nov 28 01:42:35 2024 -0800
    Workaround for CIRM-01 handles dynamic link issues that made it not work to push to public cirm. Now I have tested it and made alpha and synced web stuff to public cirm. They are all working.
  • lines changed 1, context: html, text, full: html, text
    c78ff5573c31cc5a0721db71ce24e548c40328e0 Thu Dec 12 14:21:15 2024 -0800
    relink with HAL using the updated SSL (Bug #34949)
• src/lib/https.c
  • lines changed 15, context: html, text, full: html, text
    29254dd3bfbe219e62d70ca11339f96b8a982790 Wed Dec 11 01:19:31 2024 -0800
    Fix for https cert locations on Ubuntu/Debian.
  • lines changed 2, context: html, text, full: html, text
    575e979c590a70e436e191eb91b26a23520d15e1 Wed Dec 11 01:49:20 2024 -0800
    use functions available in openssl 1.1
  • lines changed 112, context: html, text, full: html, text
    4756d333db5def5dcfdbbd4f739829bc10b432b5 Wed Dec 11 22:29:40 2024 -0800
    updating the https whitelist with a fresh scan of the last years log of the RR and Offical Mirrors.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    7d4643acb23320ce76231d38d8b8470b35bf117f Mon Dec 16 11:16:44 2024 -0800
    v476 preview1, refs #34871

• lines changed: 1826
• files changed: 62