All File Changes

v422_preview2 to v422_base (2021-10-11 to 2021-10-18) v422

• confs/hgwdev.hg.conf
  • lines changed 6, context: html, text, full: html, text
    fe44d1ead6cd1f7481db5a8e14e3d160b6198813 Sun Oct 17 01:11:36 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 3, context: html, text, full: html, text
    417a8f7efb49d9669e6252ac4f6d4e2162cbd158 Mon Oct 11 11:36:09 2021 -0700
    Minor spellling corrections based on CR, refs #28311
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 3, context: html, text, full: html, text
    3bff5347fbcb13f51d78425f0c53009cd466f8b8 Fri Oct 15 09:46:33 2021 -0700
    Auspice JSON: define ORF1ab not ORF1a/ORF1b as suggested by Cornelius Roemer in https://github.com/yatisht/usher/issues/174
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 23, context: html, text, full: html, text
    d170e9c72cc042ed0e1dccb657568b7fa14a17a1 Fri Oct 15 09:47:39 2021 -0700
    Instead of making super-long custom track names by concatenating sequence names, name the custom tracks after numbered subtrees since those are also displayed in the results table.
• src/hg/hgTracks/barChartTrack.c
  • lines changed 7, context: html, text, full: html, text
    7d448227a9ce33288ecae8cbf6d9a9ef0111c034 Thu Oct 14 00:33:49 2021 -0700
    Needed to wait until the process had gotten further than track loading before using ss spaceSaver. fixes #28291
  • lines changed 3, context: html, text, full: html, text
    80f348023d2e4c4a7fd37c5d7999b712e11f9e94 Thu Oct 14 16:54:46 2021 -0700
    Fixing barChartTrack with little tweak to wait until extras has been initialized, the track heights methods would ideally never be called BEFORE trackLoading is complete. refs #28291
• src/hg/hgTracks/gtexTracks.c
  • lines changed 3, context: html, text, full: html, text
    7d448227a9ce33288ecae8cbf6d9a9ef0111c034 Thu Oct 14 00:33:49 2021 -0700
    Needed to wait until the process had gotten further than track loading before using ss spaceSaver. fixes #28291
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ac2ee9bd9e4beb80bedcdd1783580d2eb0cb888a Thu Oct 14 00:36:31 2021 -0700
    avoiding cutting off one character in hgTracks search box, refs #28072
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    8268f8067b6ad8a5e0b0f426bedc16e567ae116a Sun Oct 3 13:38:16 2021 -0700
    fixed typo in make variable names that keeps it from being used as a environment variable
• src/hg/hgc/bigBedClick.c
  • lines changed 6, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 2, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/hgc/hgc.c
  • lines changed 53, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 1, context: html, text, full: html, text
    afd254775c46b9cecd70c11e42bc6ce011bff214 Mon Oct 11 23:03:46 2021 -0700
    fixing typo for Chris Lee.
• src/hg/hgc/hgc.h
  • lines changed 1, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 7, context: html, text, full: html, text
    f335ab4a92a1cca794160f6ac5d2ae0e0944388b Fri Oct 15 17:02:59 2021 -0700
    Adding an example rsync path that users can try, and a mention of the euro server for ftp, refs #28327
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 26, context: html, text, full: html, text
    f02d4b878d5152858b15c2f847b6824cf436ef0e Wed Oct 13 14:30:28 2021 -0700
    Announcing VOC track update refs #27926
• src/hg/htdocs/images/spikeProPro.jpg
  • lines changed 0, context: html, text, full: html, text
    6ac608972f07276c4088851ed911334fec9afd3e Mon Oct 11 14:09:16 2021 -0700
    adding details about open house and virus vaccine browser image
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    f02d4b878d5152858b15c2f847b6824cf436ef0e Wed Oct 13 14:30:28 2021 -0700
    Announcing VOC track update refs #27926
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 58, context: html, text, full: html, text
    8cb0587b8d832eff7322c595c8547e4655569119 Mon Oct 18 07:22:55 2021 -0700
    fixing LOVD otto job, also must check for total size, I forgot at the time the most basic check. No redmine yet, email from Bob
• src/hg/htdocs/training/openHouse.html
  • lines changed 28, context: html, text, full: html, text
    6ac608972f07276c4088851ed911334fec9afd3e Mon Oct 11 14:09:16 2021 -0700
    adding details about open house and virus vaccine browser image
  • lines changed 3, context: html, text, full: html, text
    078c7a4b342ffd2ef7449251b30d8577abb34c33 Tue Oct 12 01:53:27 2021 -0700
    small wording changes to openhouse html, no redmine
  • lines changed 5, context: html, text, full: html, text
    7009775e77d5193439a9f3a2aad859b240b2b803 Wed Oct 13 10:33:45 2021 -0700
    adding link to staff page
  • lines changed 3, context: html, text, full: html, text
    6fac208fd9d6fe2ee23c043a78559e252f39cf7b Mon Oct 18 09:20:09 2021 -0700
    added link to help image about breakout rooms
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5b02224b48e2c6dce7767559d08ebaa2798b678d Mon Oct 18 10:08:45 2021 -0700
    New version number v422
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    5ee9095a2645bf0ee44026f11063d523fe1d51a9 Tue Oct 12 02:57:29 2021 -0700
    adding oxford comma to watermark, refs #28072
• src/hg/js/ddcl.js
  • lines changed 4, context: html, text, full: html, text
    cae42c43b9cd412f15cc7913e82a319cb9db3f15 Fri Oct 15 13:02:39 2021 -0700
    Fix overflow of filter list in hgTrackUi pop ups, refs #28176
• src/hg/js/hgHubConnect.js
  • lines changed 55, context: html, text, full: html, text
    8cb0587b8d832eff7322c595c8547e4655569119 Mon Oct 18 07:22:55 2021 -0700
    fixing LOVD otto job, also must check for total size, I forgot at the time the most basic check. No redmine yet, email from Bob
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 46, context: html, text, full: html, text
    ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700
    import of all gencode v39lift37
  • lines changed 1, context: html, text, full: html, text
    ec9318204bf7a42acd791c03d0a6f93393843bd7 Sun Oct 17 10:12:22 2021 -0700
    fixed typo in build doc
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 34, context: html, text, full: html, text
    a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700
    import of gencode V39 pre-release
  • lines changed 1, context: html, text, full: html, text
    4e0ba60ac25fa6a44e6446852ce5c2aeda68d757 Fri Oct 15 17:18:43 2021 -0700
    fixed gencode release date
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 47, context: html, text, full: html, text
    8979882863a20beb00f7c72cfc4263a1e5a9863b Fri Oct 15 15:28:44 2021 -0700
    Updating gtex README with latest version of script and other details about latest version of the track. Also tweaking track description page to be more accurate, refs #27947
  • lines changed 4, context: html, text, full: html, text
    557e23cb23716c1e543903446c03bb3ed7a5a195 Fri Oct 15 15:31:42 2021 -0700
    adding details about other files used, refs #27947
• src/hg/makeDb/doc/hg38/patchUpdate.13.txt
  • lines changed 4, context: html, text, full: html, text
    705126cb1d2946056b9da0397acaf2bb6703c6e4 Tue Oct 12 22:43:02 2021 -0700
    finishing off GRC incident step now that QA has pushed hg38.2bit to RR. refs #25091
• src/hg/makeDb/doc/hg38/ucscToEnsembl.txt
  • lines changed 222, context: html, text, full: html, text
    b1877bec9f5132370e0ef24ba7cbb10e33f9c623 Mon Oct 11 15:15:37 2021 -0700
    constructing the ucscToEnsembl and ensemblLift tables refs #25091
• src/hg/makeDb/doc/macFas5/lastzRuns.txt
  • lines changed 102, context: html, text, full: html, text
    e29a2749a1dd0fc28c17cd45270edbf151cbd532 Wed Oct 13 10:11:15 2021 -0700
    per user request rheMac2 and rheMac10 chainNet to macFas5 refs #28318
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 37, context: html, text, full: html, text
    e1b0f07ffbe7508b97259a9d3c28956152bacfa9 Sat Oct 16 16:55:27 2021 -0700
    import of All gencode VM28
• src/hg/makeDb/doc/rheMac10/lastzRuns.txt
  • lines changed 101, context: html, text, full: html, text
    e29a2749a1dd0fc28c17cd45270edbf151cbd532 Wed Oct 13 10:11:15 2021 -0700
    per user request rheMac2 and rheMac10 chainNet to macFas5 refs #28318
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
  • lines changed 3, context: html, text, full: html, text
    84ea45f07d5971e1d97618675a923056d41995db Mon Oct 11 11:47:46 2021 -0700
    Clarify make doc. refs #27926
• src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
  • lines changed 103, context: html, text, full: html, text
    676d7fc25a5c8533edd747f23ef7a526f45468d0 Sat Oct 16 16:52:45 2021 -0700
    switch to using chromAlias table for getting mappings (thanks Hiram)
  • lines changed 3, context: html, text, full: html, text
    6606cc2195a5299cf1cea8e2de7661e57c7ac67f Sat Oct 16 17:30:05 2021 -0700
    don't restrict chromAlias entries, as some ensembl ones are omitted to to strand swap
  • lines changed 5, context: html, text, full: html, text
    e949d9121dea4c10ccce47ff7a781df9b0f01813 Sat Oct 16 18:51:58 2021 -0700
    ignore contamination unplaced chromsome in GRCh38
  • lines changed 3, context: html, text, full: html, text
    ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700
    import of all gencode v39lift37
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 11, context: html, text, full: html, text
    a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700
    import of gencode V39 pre-release
  • lines changed 16, context: html, text, full: html, text
    e1b0f07ffbe7508b97259a9d3c28956152bacfa9 Sat Oct 16 16:55:27 2021 -0700
    import of All gencode VM28
  • lines changed 4, context: html, text, full: html, text
    ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700
    import of all gencode v39lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 95, context: html, text, full: html, text
    a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700
    import of gencode V39 pre-release
  • lines changed 95, context: html, text, full: html, text
    e1b0f07ffbe7508b97259a9d3c28956152bacfa9 Sat Oct 16 16:55:27 2021 -0700
    import of All gencode VM28
  • lines changed 90, context: html, text, full: html, text
    ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700
    import of all gencode v39lift37
• src/hg/makeDb/trackDb/chicken/galGal6/crispr10K.ra
  • lines changed 1, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 1, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/crispr10K.ra
  • lines changed 1, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 1, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/crisprAll.ra
  • lines changed 1, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 1, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/human/gtexCov.html
  • lines changed 144, context: html, text, full: html, text
    2bd5a55547bf3e1c1b95622b6bb7dcd7cb4d2369 Wed Oct 13 07:31:15 2021 -0700
    finishing up gtex rna-seq coverage track, refs #27964
• src/hg/makeDb/trackDb/human/gtexCov.ra
  • lines changed 57, context: html, text, full: html, text
    2bd5a55547bf3e1c1b95622b6bb7dcd7cb4d2369 Wed Oct 13 07:31:15 2021 -0700
    finishing up gtex rna-seq coverage track, refs #27964
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.html
  • lines changed 32, context: html, text, full: html, text
    ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700
    import of all gencode v39lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.ra
  • lines changed 224, context: html, text, full: html, text
    ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700
    import of all gencode v39lift37
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 3, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 1, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/human/hg38/gtexEqtlHighConf.html
  • lines changed 1, context: html, text, full: html, text
    8979882863a20beb00f7c72cfc4263a1e5a9863b Fri Oct 15 15:28:44 2021 -0700
    Updating gtex README with latest version of script and other details about latest version of the track. Also tweaking track description page to be more accurate, refs #27947
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700
    import of gencode V39 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.html
  • lines changed 47, context: html, text, full: html, text
    a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700
    import of gencode V39 pre-release
  • lines changed 1, context: html, text, full: html, text
    4e0ba60ac25fa6a44e6446852ce5c2aeda68d757 Fri Oct 15 17:18:43 2021 -0700
    fixed gencode release date
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.ra
  • lines changed 286, context: html, text, full: html, text
    a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700
    import of gencode V39 pre-release
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 2, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    32ff80a3c1fba843c93106505abb1dcf0ad7f91c Sat Oct 16 17:31:11 2021 -0700
    forgot to include new ra file
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.html
  • lines changed 30, context: html, text, full: html, text
    e1b0f07ffbe7508b97259a9d3c28956152bacfa9 Sat Oct 16 16:55:27 2021 -0700
    import of All gencode VM28
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.ra
  • lines changed 286, context: html, text, full: html, text
    e1b0f07ffbe7508b97259a9d3c28956152bacfa9 Sat Oct 16 16:55:27 2021 -0700
    import of All gencode VM28
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 1, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 94, context: html, text, full: html, text
    427071eec197d9d78a25a56610b08d46a22d957f Fri Oct 15 14:18:17 2021 -0700
    completed chainNet for GCF_016699485.2 refs #28336
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
  • lines changed 2, context: html, text, full: html, text
    8b58465d5ad8b68854a9a6fb938dff07e23650f6 Tue Oct 12 10:12:06 2021 -0700
    Adding pennantIcons for hg38 patch 13 release, refs #25091
  • lines changed 1, context: html, text, full: html, text
    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    5dfb1c58d342b625f6dccb8651793ec9315a755e Mon Oct 11 16:52:10 2021 -0700
    Adding notes to VOC track refs #27926
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.html
  • lines changed 51, context: html, text, full: html, text
    5dfb1c58d342b625f6dccb8651793ec9315a755e Mon Oct 11 16:52:10 2021 -0700
    Adding notes to VOC track refs #27926
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.ra
  • lines changed 30, context: html, text, full: html, text
    5dfb1c58d342b625f6dccb8651793ec9315a755e Mon Oct 11 16:52:10 2021 -0700
    Adding notes to VOC track refs #27926
  • lines changed 1, context: html, text, full: html, text
    f11e78afb7d51bc3277b179c717f22317433744c Mon Oct 11 18:09:03 2021 -0700
    Changing label refs #27926
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    5d7cbea137ba4f0b1c11fbc11ca453fa49fd66ed Wed Oct 13 11:22:55 2021 -0700
    Updating html to point to correct file and shortLabel refs #27676
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
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    e408d52de2f812c4dc407b1865c97c45090dcf16 Mon Oct 11 16:40:46 2021 -0700
    Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible
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    de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 Thu Oct 14 15:46:17 2021 -0700
    Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335
• src/hg/phyloPng/makefile
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    b275bed5b8219c6f88a98602a5e82d1655166415 Sun Oct 3 13:42:11 2021 -0700
    fixed rule that copies phyloPng to a BINDIR to take from the correct CGI dir
• src/hg/utils/automation/gpToIx.pl
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    fa023b2cfad8f6c0b0482dc7d89849d6d645077f Wed Oct 13 12:22:54 2021 -0700
    attempt to better manage NCBI names no redmine
• src/hg/utils/automation/pairLastz.sh
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    c1c72d06c1897453aa237aa30124d66a14464f59 Wed Oct 13 10:12:40 2021 -0700
    fixup the primate to primate DEF file and begin to add the auto detection of which should be target vs query refs #28318
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    bea909cab25eb4b528961e6df5c48146fda7722f Tue Oct 12 06:10:45 2021 -0700
    hacking around letsencrypt issue in LOVD otto job temporarily, until Galt or the admins do something to fix this long-term, no redmine, email with Lou
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    8cb0587b8d832eff7322c595c8547e4655569119 Mon Oct 18 07:22:55 2021 -0700
    fixing LOVD otto job, also must check for total size, I forgot at the time the most basic check. No redmine yet, email from Bob
• src/hg/utils/otto/lovd/download.sh
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    bea909cab25eb4b528961e6df5c48146fda7722f Tue Oct 12 06:10:45 2021 -0700
    hacking around letsencrypt issue in LOVD otto job temporarily, until Galt or the admins do something to fix this long-term, no redmine, email with Lou
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    c1595df4f78382977a7a8ae96f233b8541bf4ce7 Tue Oct 12 16:19:55 2021 -0700
    Removing the insecure k flag as it seems lovd have updated their servers refs #28328
• src/hg/utils/otto/lovd/makefile
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    17ce4a2dceebb009e4f949c8c875ef453e58c66c Tue Oct 12 16:22:13 2021 -0700
    Updating makefile with new .as files, change happened long ago but makefile was not updated.
• src/hg/utils/otto/sarscov2phylo/util.sh
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    ad6e3b51842fe726bb9b14e3b0025e59ef9fda17 Fri Oct 15 09:48:41 2021 -0700
    More items for cleanGenBank to detect & substitute.
• src/inc/cgi_build_rules.mk
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    8268f8067b6ad8a5e0b0f426bedc16e567ae116a Sun Oct 3 13:38:16 2021 -0700
    fixed typo in make variable names that keeps it from being used as a environment variable
• src/inc/srcVersion.h
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    5b02224b48e2c6dce7767559d08ebaa2798b678d Mon Oct 18 10:08:45 2021 -0700
    New version number v422
• src/lib/https.c
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    ea0ea7155718c9acacc21f07b2d8cd247a2e9707 Tue Oct 12 17:21:06 2021 -0700
    Add trust_first flag to https.c for verify makes openssl 1.0 compatible with LetsEncrypt flags. fixes #28332
• src/product/installer/browserSetup.sh
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    937684478679eb2fa4ef180017a0bc8ed762f0ac Mon Oct 18 08:39:48 2021 -0700
    fixing GBIC on newer linux distributions that use Mysql 8 by default now, refs #28348
• src/utils/bigBedToBed/bigBedToBed.c
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    5b19f269d7e89acb83b34ad0ffeb1f6451a8210b Sun Oct 17 19:32:25 2021 -0700
    added option to bigBedToBed to write autoSql style column header
• src/utils/qa/weeklybld/buildEnv.csh
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    01f4c1ea296441f023e2717351d7d007fcfda094 Mon Oct 18 10:08:03 2021 -0700
    v422 final build, refs #28292

• lines changed: 2838
• files changed: 101