All File Changes

v447_base to v448_preview (2023-04-24 to 2023-05-01) v448

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3772c83b39f739b12b2b269fe06feb45ab549d9a Sun Apr 30 01:11:28 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3772c83b39f739b12b2b269fe06feb45ab549d9a Sun Apr 30 01:11:28 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 6, context: html, text, full: html, text
    3772c83b39f739b12b2b269fe06feb45ab549d9a Sun Apr 30 01:11:28 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 15, context: html, text, full: html, text
    3772c83b39f739b12b2b269fe06feb45ab549d9a Sun Apr 30 01:11:28 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3772c83b39f739b12b2b269fe06feb45ab549d9a Sun Apr 30 01:11:28 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    660c13fee76b94704905eaf5c248579cc18ad5db Wed Apr 26 16:56:18 2023 -0700
    Erase leading and trailing whitespace from hgGateway database search string, refs #30257
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    6412b58f4efb9beba7d01f8cf50f6026d0188436 Thu Apr 27 13:31:02 2023 -0700
    fix a couple of bugs in squishyPack mode
• src/hg/hgTracks/snake.c
  • lines changed 32, context: html, text, full: html, text
    faafcf1c5f1b1da28a628d6e9aa7ab9d3ee455a8 Fri Apr 28 12:13:01 2023 -0700
    fix pack mode
• src/hg/hgc/hgc.c
  • lines changed 30, context: html, text, full: html, text
    73e6200cac3a877472fa393fb6cbeb6e43be9f5a Sat Apr 29 15:30:40 2023 -0700
    some work on hgc page for chains in snake mode
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 19, context: html, text, full: html, text
    f551cdfc0ad0192789b53b68089791441a3e4277 Fri Apr 28 14:55:57 2023 -0700
    fixing mirrorManual.html, after code review, refs #31101
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 17, context: html, text, full: html, text
    a393477280e41c81f19756a99ba3574293c8b994 Mon Apr 24 16:36:12 2023 -0700
    Announcing the release of the hg38 DGV gold track, refs #30908
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a393477280e41c81f19756a99ba3574293c8b994 Mon Apr 24 16:36:12 2023 -0700
    Announcing the release of the hg38 DGV gold track, refs #30908
• src/hg/inc/trackDb.h
  • lines changed 2, context: html, text, full: html, text
    6412b58f4efb9beba7d01f8cf50f6026d0188436 Thu Apr 27 13:31:02 2023 -0700
    fix a couple of bugs in squishyPack mode
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    6412b58f4efb9beba7d01f8cf50f6026d0188436 Thu Apr 27 13:31:02 2023 -0700
    fix a couple of bugs in squishyPack mode
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    9f00cd98a12cc7a8127db406db7e072763c2175a Tue Apr 25 10:28:40 2023 -0700
    changed "No subtracks in group:" message to include track name
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    ede53f2613a6939bd314dceef806297ffd955ff7 Mon Apr 24 18:08:43 2023 -0700
    adding 1 per user request and 1 for CCGP refs #29545 #30508
  • lines changed 12, context: html, text, full: html, text
    de34bc0db1a0b760102100212c05b69353c84a9d Tue Apr 25 14:15:18 2023 -0700
    almost done with CCGP update refs #30508
  • lines changed 1, context: html, text, full: html, text
    4353fbea684d6bab1dc5658ea60164e74d78d9b1 Fri Apr 28 13:21:02 2023 -0700
    adding one CCGP assembly to finish up the first batch refs #30508
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    aaf0fe88d4968aa5f16b0ffc07fdefe1bea1c7cb Tue Apr 25 15:03:48 2023 -0700
    catching up CCGP assemblies refs #30508
  • lines changed 12, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
  • lines changed 38, context: html, text, full: html, text
    aaf0fe88d4968aa5f16b0ffc07fdefe1bea1c7cb Tue Apr 25 15:03:48 2023 -0700
    catching up CCGP assemblies refs #30508
  • lines changed 2, context: html, text, full: html, text
    4353fbea684d6bab1dc5658ea60164e74d78d9b1 Fri Apr 28 13:21:02 2023 -0700
    adding one CCGP assembly to finish up the first batch refs #30508
  • lines changed 16, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.taxId.asmId.class.txt
  • lines changed 65, context: html, text, full: html, text
    059f136979c8b868b2b909f4d127daa67130651e Tue Apr 25 15:04:23 2023 -0700
    catching up CCGP assemblies refs #30508
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 35, context: html, text, full: html, text
    584d70ac259b9b2f818e40a2f838ac114e4b234d Tue Apr 25 19:58:18 2023 -0700
    import of gencode V44 pre-release
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ede53f2613a6939bd314dceef806297ffd955ff7 Mon Apr 24 18:08:43 2023 -0700
    adding 1 per user request and 1 for CCGP refs #29545 #30508
  • lines changed 1, context: html, text, full: html, text
    aaf0fe88d4968aa5f16b0ffc07fdefe1bea1c7cb Tue Apr 25 15:03:48 2023 -0700
    catching up CCGP assemblies refs #30508
  • lines changed 6, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ede53f2613a6939bd314dceef806297ffd955ff7 Mon Apr 24 18:08:43 2023 -0700
    adding 1 per user request and 1 for CCGP refs #29545 #30508
  • lines changed 7, context: html, text, full: html, text
    aaf0fe88d4968aa5f16b0ffc07fdefe1bea1c7cb Tue Apr 25 15:03:48 2023 -0700
    catching up CCGP assemblies refs #30508
  • lines changed 2, context: html, text, full: html, text
    4353fbea684d6bab1dc5658ea60164e74d78d9b1 Fri Apr 28 13:21:02 2023 -0700
    adding one CCGP assembly to finish up the first batch refs #30508
  • lines changed 9, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 36, context: html, text, full: html, text
    7fb2f3f334694376f7bec47237552ddf8eb186dc Wed Apr 26 10:13:42 2023 -0700
    import of gencode VM33 prerelease
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    aaf0fe88d4968aa5f16b0ffc07fdefe1bea1c7cb Tue Apr 25 15:03:48 2023 -0700
    catching up CCGP assemblies refs #30508
  • lines changed 23, context: html, text, full: html, text
    629e5f28b4eb06707240093a386286abf1a5ec8d Fri Apr 28 14:35:07 2023 -0700
    catch up CCGP assemblies in their respective GenArk groups refs #30508
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
  • lines changed 2, context: html, text, full: html, text
    584d70ac259b9b2f818e40a2f838ac114e4b234d Tue Apr 25 19:58:18 2023 -0700
    import of gencode V44 pre-release
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 10, context: html, text, full: html, text
    584d70ac259b9b2f818e40a2f838ac114e4b234d Tue Apr 25 19:58:18 2023 -0700
    import of gencode V44 pre-release
  • lines changed 2, context: html, text, full: html, text
    7fb2f3f334694376f7bec47237552ddf8eb186dc Wed Apr 26 10:13:42 2023 -0700
    import of gencode VM33 prerelease
• src/hg/makeDb/schema/all.joiner
  • lines changed 94, context: html, text, full: html, text
    584d70ac259b9b2f818e40a2f838ac114e4b234d Tue Apr 25 19:58:18 2023 -0700
    import of gencode V44 pre-release
  • lines changed 94, context: html, text, full: html, text
    7fb2f3f334694376f7bec47237552ddf8eb186dc Wed Apr 26 10:13:42 2023 -0700
    import of gencode VM33 prerelease
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    ae4233f85eae7917fa2d5cb56b21466ec30dae4b Mon Apr 24 12:18:28 2023 -0700
    Adding the frequency to the mouse overs, feedback from Ana refs #30908
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    7fb2f3f334694376f7bec47237552ddf8eb186dc Wed Apr 26 10:13:42 2023 -0700
    import of gencode VM33 prerelease
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    ae4233f85eae7917fa2d5cb56b21466ec30dae4b Mon Apr 24 12:18:28 2023 -0700
    Adding the frequency to the mouse overs, feedback from Ana refs #30908
  • lines changed 2, context: html, text, full: html, text
    a393477280e41c81f19756a99ba3574293c8b994 Mon Apr 24 16:36:12 2023 -0700
    Announcing the release of the hg38 DGV gold track, refs #30908
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV44.html
  • lines changed 47, context: html, text, full: html, text
    584d70ac259b9b2f818e40a2f838ac114e4b234d Tue Apr 25 19:58:18 2023 -0700
    import of gencode V44 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV44.ra
  • lines changed 247, context: html, text, full: html, text
    584d70ac259b9b2f818e40a2f838ac114e4b234d Tue Apr 25 19:58:18 2023 -0700
    import of gencode V44 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    98f6898ff0f6b691240aee086f1b5282044dca76 Wed Apr 26 10:16:15 2023 -0700
    add mouse gencode to parent ra
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM33.html
  • lines changed 30, context: html, text, full: html, text
    7fb2f3f334694376f7bec47237552ddf8eb186dc Wed Apr 26 10:13:42 2023 -0700
    import of gencode VM33 prerelease
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM33.ra
  • lines changed 247, context: html, text, full: html, text
    7fb2f3f334694376f7bec47237552ddf8eb186dc Wed Apr 26 10:13:42 2023 -0700
    import of gencode VM33 prerelease
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
  • lines changed 8, context: html, text, full: html, text
    9f00cd98a12cc7a8127db406db7e072763c2175a Tue Apr 25 10:28:40 2023 -0700
    changed "No subtracks in group:" message to include track name
• src/product/installer/browserSetup.sh
  • lines changed 6, context: html, text, full: html, text
    e254083e7f7e36e3d4ddc2324dbe622b8407a887 Mon Apr 24 14:21:27 2023 -0700
    Have GBiC automatically make the cram cache directories on install, refs Lon email
  • lines changed 1, context: html, text, full: html, text
    07c5c1d8d8dc3f88fbc8792278bd34e6cda9ef38 Mon Apr 24 16:11:35 2023 -0700
    Contributed by user DailyDreaming on github.
• src/userApps/fetchKentSource.sh
  • lines changed 1, context: html, text, full: html, text
    4a568aec7679647ea8d195ac4e303de461f6c71e Mon Apr 24 14:11:07 2023 -0700
    adding src/optimalLeaf directory to the fetch source no redmine
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    afc989589da6ac5533348f7b6f3de1d97fc2860f Mon May 1 10:05:22 2023 -0700
    v448 preview1, refs #31125

• lines changed: 1244
• files changed: 56