All File Changes

v420_base to v421_preview (2021-09-07 to 2021-09-13) v421

• confs/hgwbeta-public.hg.conf
  • lines changed 2, context: html, text, full: html, text
    8b04fd7d06c10259862e8e70099ddbdb6aede88e Sun Sep 12 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 7, context: html, text, full: html, text
    8b04fd7d06c10259862e8e70099ddbdb6aede88e Sun Sep 12 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/bestPractices.html
  • lines changed 407, context: html, text, full: html, text
    171f3bb0dc5a9d50b62de57de845c014739f24c7 Tue Sep 7 16:01:01 2021 -0700
    Adding Tiana's diagrams to page, no redmine
• src/hg/hgCustom/hgCustom.c
  • lines changed 5, context: html, text, full: html, text
    64390d995b22c5399966675834f1eb2132deb4e6 Wed Sep 8 02:01:02 2021 -0700
    small wording change to hgCustom help text, no redmine, just noticed that it is hard to see this text among the ton of other text. This input box probably has too much text now.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 6, context: html, text, full: html, text
    1813d94a8d9108b9709cb48166b4980d0f02d839 Wed Sep 8 12:02:05 2021 -0700
    Add coloring options for Nextstrain clade and Pango lineage assigned by usher (really by matUtils annotate) if metadata includes columns for those.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 4, context: html, text, full: html, text
    1813d94a8d9108b9709cb48166b4980d0f02d839 Wed Sep 8 12:02:05 2021 -0700
    Add coloring options for Nextstrain clade and Pango lineage assigned by usher (really by matUtils annotate) if metadata includes columns for those.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 12, context: html, text, full: html, text
    15b84072ef48791ec41cb031ef351997c3dee4d7 Tue Sep 7 15:15:17 2021 -0700
    Added a new branch label option: back-mutations to reference, to highlight problematic parts of the tree.
  • lines changed 78, context: html, text, full: html, text
    1813d94a8d9108b9709cb48166b4980d0f02d839 Wed Sep 8 12:02:05 2021 -0700
    Add coloring options for Nextstrain clade and Pango lineage assigned by usher (really by matUtils annotate) if metadata includes columns for those.
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    f4a41965d1f5c26bcae644bba6777e141d485a95 Wed Sep 8 01:56:09 2021 -0700
    merging highlight-color-sticking into master, refs #28098 Squashed commit of the following: commit f09bd0dcc1c23a91aae3c07610066b28e5177d82 Author: Max <max@soe.ucsc.edu> Date: Tue Sep 7 03:02:46 2021 -0700 Adding another anonymous function, to make sure that the page load does not crash because one of the .js files is not loaded yet, refs #28090 commit 5934e12f75e610bb8ff699dc17be5743a4b17c37 Author: Max <max@soe.ucsc.edu> Date: Tue Sep 7 02:36:40 2021 -0700 Fixing a super annoying CSS bug in our dialog box where the buttons moved on hover, and adding a 'save color' button to the highlight dialogbox. Not a perfect solution, but adresses the missing save button problem at least for now, refs #28090 commit 1d6a87e7303297c61637591807b338294cc1dcec Author: Max <max@soe.ucsc.edu> Date: Thu Sep 2 08:23:00 2021 -0700 updated shift-drag dialog, refs #28090 commit 4e078c875f10d5b23d9540ec8dd3efba7b3af4c9 Author: Max <max@soe.ucsc.edu> Date: Thu Sep 2 06:35:36 2021 -0700 saving previous picked highlight color to the cart, refs #28090
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    d75b20bbdc18266a8e9eb90a6c61109648e838c4 Thu Sep 9 16:28:47 2021 -0700
    Fix extra cloneString from code review, refs #28119
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 22, context: html, text, full: html, text
    0d0a7789414e9f3571c66ffb0977eadebde86992 Thu Sep 9 03:32:48 2021 -0700
    updating faqgenes, refs #28132
  • lines changed 1, context: html, text, full: html, text
    5d4ceca3972f7cc98ceb6aee0ec02b4541d52527 Fri Sep 10 11:38:14 2021 -0700
    Updating old link to MANE, no RM
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 101, context: html, text, full: html, text
    69535d985db2e0cf42b05b5eaaae581704df5627 Thu Sep 9 18:03:41 2021 -0700
    added search box, removed bullets from topics section to match other help pages, added section for videos about links
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 91, context: html, text, full: html, text
    131c2f5bfb31233b87664c985eb361dd1b0005a2 Wed Sep 8 05:56:35 2021 -0700
    making looking for a genome assembly link stand out more using CSS, refs #26081
• src/hg/htdocs/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    2046bf2c5de3cbdb819ad4c186b8053ee1959100 Wed Sep 8 14:52:00 2021 -0700
    Adding widget to two more pages refs #28034
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    01975a2c494b690fb94245a35ec2c016a3aa93ed Thu Sep 9 16:26:57 2021 -0700
    changed level of browser lines and track lines sections to make them subsections. displayed by include in hgTracksHelp.html and customTrack.html
  • lines changed 2, context: html, text, full: html, text
    1e741586df2786bc27b6a9f86c2ac8618edcb9c3 Thu Sep 9 16:54:40 2021 -0700
    'rephrased a line and made it clear that browser lines are optional
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 1, context: html, text, full: html, text
    46bc51c8471753fe5af0a72171f008f038a33f71 Thu Sep 9 18:49:20 2021 -0700
    fixed a typo
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    2046bf2c5de3cbdb819ad4c186b8053ee1959100 Wed Sep 8 14:52:00 2021 -0700
    Adding widget to two more pages refs #28034
  • lines changed 11, context: html, text, full: html, text
    aad219b68b73b72b0e1ef012d91081b21f42158f Thu Sep 9 15:24:39 2021 -0700
    moved query bozes above the fold to be more obvious
  • lines changed 2, context: html, text, full: html, text
    3a1dad7107c1eced5debd13372747f42853c4211 Thu Sep 9 16:28:26 2021 -0700
    added a couple of landmarks to make it easier to get around in file
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 11, context: html, text, full: html, text
    10bb49ac599fb3b14966b832cc4992673db5394f Wed Sep 8 22:35:27 2021 -0700
    added links to vids on the page from within text sections
  • lines changed 10, context: html, text, full: html, text
    ffb371e4dab8c6c689bc4b9d6bc8b95806deb91e Thu Sep 9 17:12:56 2021 -0700
    moved search box up closer to top of page
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 4, context: html, text, full: html, text
    131c2f5bfb31233b87664c985eb361dd1b0005a2 Wed Sep 8 05:56:35 2021 -0700
    making looking for a genome assembly link stand out more using CSS, refs #26081
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 1, context: html, text, full: html, text
    f4a41965d1f5c26bcae644bba6777e141d485a95 Wed Sep 8 01:56:09 2021 -0700
    merging highlight-color-sticking into master, refs #28098 Squashed commit of the following: commit f09bd0dcc1c23a91aae3c07610066b28e5177d82 Author: Max <max@soe.ucsc.edu> Date: Tue Sep 7 03:02:46 2021 -0700 Adding another anonymous function, to make sure that the page load does not crash because one of the .js files is not loaded yet, refs #28090 commit 5934e12f75e610bb8ff699dc17be5743a4b17c37 Author: Max <max@soe.ucsc.edu> Date: Tue Sep 7 02:36:40 2021 -0700 Fixing a super annoying CSS bug in our dialog box where the buttons moved on hover, and adding a 'save color' button to the highlight dialogbox. Not a perfect solution, but adresses the missing save button problem at least for now, refs #28090 commit 1d6a87e7303297c61637591807b338294cc1dcec Author: Max <max@soe.ucsc.edu> Date: Thu Sep 2 08:23:00 2021 -0700 updated shift-drag dialog, refs #28090 commit 4e078c875f10d5b23d9540ec8dd3efba7b3af4c9 Author: Max <max@soe.ucsc.edu> Date: Thu Sep 2 06:35:36 2021 -0700 saving previous picked highlight color to the cart, refs #28090
• src/hg/js/hgTracks.js
  • lines changed 70, context: html, text, full: html, text
    f4a41965d1f5c26bcae644bba6777e141d485a95 Wed Sep 8 01:56:09 2021 -0700
    merging highlight-color-sticking into master, refs #28098 Squashed commit of the following: commit f09bd0dcc1c23a91aae3c07610066b28e5177d82 Author: Max <max@soe.ucsc.edu> Date: Tue Sep 7 03:02:46 2021 -0700 Adding another anonymous function, to make sure that the page load does not crash because one of the .js files is not loaded yet, refs #28090 commit 5934e12f75e610bb8ff699dc17be5743a4b17c37 Author: Max <max@soe.ucsc.edu> Date: Tue Sep 7 02:36:40 2021 -0700 Fixing a super annoying CSS bug in our dialog box where the buttons moved on hover, and adding a 'save color' button to the highlight dialogbox. Not a perfect solution, but adresses the missing save button problem at least for now, refs #28090 commit 1d6a87e7303297c61637591807b338294cc1dcec Author: Max <max@soe.ucsc.edu> Date: Thu Sep 2 08:23:00 2021 -0700 updated shift-drag dialog, refs #28090 commit 4e078c875f10d5b23d9540ec8dd3efba7b3af4c9 Author: Max <max@soe.ucsc.edu> Date: Thu Sep 2 06:35:36 2021 -0700 saving previous picked highlight color to the cart, refs #28090
• src/hg/lib/bedDetail.c
  • lines changed 5, context: html, text, full: html, text
    fefdc562bc014756f3c22f53dce16126ada37b56 Wed Sep 8 11:09:33 2021 -0700
    update bad blocks message to read as documentation refs #28131
• src/hg/lib/customFactory.c
  • lines changed 5, context: html, text, full: html, text
    fefdc562bc014756f3c22f53dce16126ada37b56 Wed Sep 8 11:09:33 2021 -0700
    update bad blocks message to read as documentation refs #28131
• src/hg/lib/encode/encodePeak.c
  • lines changed 5, context: html, text, full: html, text
    fefdc562bc014756f3c22f53dce16126ada37b56 Wed Sep 8 11:09:33 2021 -0700
    update bad blocks message to read as documentation refs #28131
• src/hg/lib/hgHgvs.c
  • lines changed 6, context: html, text, full: html, text
    2d503f8823cbee3db01fc029b2ae42701e36469b Fri Sep 10 11:46:47 2021 -0700
    Fix crash when hgvsParseTerm fails to find a match to a psuedo hgvs term, refs #28147
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    4e69c248540a8df5731f625e9522968d33559107 Thu Sep 9 08:29:06 2021 -0700
    Adding closing </b> tag to printf statement for filters, refs #28106
  • lines changed 2, context: html, text, full: html, text
    d1377e8f79200627fd93012f73e32bdd0ae2de5f Thu Sep 9 13:22:39 2021 -0700
    use filterLabel for text filters instead of field name
  • lines changed 11, context: html, text, full: html, text
    a6fc30fa49ef07dc75cdeff0423b7b70fe28889d Thu Sep 9 13:53:50 2021 -0700
    oops.. a little polish on the previous commit
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 51, context: html, text, full: html, text
    8159a5952f6e31625a4e2ad08054685065b36be4 Fri Sep 10 13:48:12 2021 -0700
    Adding makedoc for GTEx cis-eQTL track, refs #27947
• src/hg/makeDb/doc/hg38/mane.txt
  • lines changed 9, context: html, text, full: html, text
    038d6e68ca59681d6cf608de90cfd7e1b8cb9c98 Thu Sep 9 17:30:45 2021 -0700
    adding MANE v 0.95
• src/hg/makeDb/doc/hg38/multiz100way.txt
  • lines changed 13, context: html, text, full: html, text
    a2fba51d8eda61736f4c5cf2e40bc7fc12a9e5ee Sat Sep 11 07:26:05 2021 -0700
    rebuilt V38 mafGene downloads for hg38
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV36.sh
  • lines changed 5, context: html, text, full: html, text
    a58598681583d3b1637c0a9fcd25610bdf2b6566 Sat Sep 11 07:27:43 2021 -0700
    some cleanup of this old doc file
• src/hg/makeDb/trackDb/human/hg38/bloodHao.html
  • lines changed 18, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/bloodHao.ra
  • lines changed 12, context: html, text, full: html, text
    fee40f46d55d92f748841141af7e7f831376a51c Wed Sep 8 13:26:33 2021 -0700
    Added link to Cell Browser. refs #26965
• src/hg/makeDb/trackDb/human/hg38/colonWang.html
  • lines changed 5, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/colonWang.ra
  • lines changed 4, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.html
  • lines changed 21, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra
  • lines changed 10, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 4, context: html, text, full: html, text
    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
  • lines changed 28, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra
  • lines changed 18, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/genePredArchive.ra
  • lines changed 2, context: html, text, full: html, text
    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
• src/hg/makeDb/trackDb/human/hg38/gtexEqtl.ra
  • lines changed 15, context: html, text, full: html, text
    c138b5ec2061de1ba8a4eeb89e49e53711265dee Wed Sep 8 11:13:40 2021 -0700
    Initial add of hg38 GTEx tracks. refs #27947
  • lines changed 1, context: html, text, full: html, text
    21e7028c87a7e72e50602f56fa354c43bd193a5b Thu Sep 9 12:18:13 2021 -0700
    Adding interactDirectional setting to gtexEqtlHighConf so that source/target labels are used, refs #27947
• src/hg/makeDb/trackDb/human/hg38/gtexEqtlHighConf.html
  • lines changed 117, context: html, text, full: html, text
    c138b5ec2061de1ba8a4eeb89e49e53711265dee Wed Sep 8 11:13:40 2021 -0700
    Initial add of hg38 GTEx tracks. refs #27947
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.html
  • lines changed 27, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra
  • lines changed 18, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/ileumWang.html
  • lines changed 5, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/ileumWang.ra
  • lines changed 4, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.html
  • lines changed 21, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra
  • lines changed 12, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/knownGeneV32.ra
  • lines changed 1, context: html, text, full: html, text
    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.html
  • lines changed 7, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra
  • lines changed 6, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.html
  • lines changed 12, context: html, text, full: html, text
    acc9bdd9e20ba89f819f963c2a9558b207288392 Tue Sep 7 09:02:28 2021 -0700
    Added missing Data Access section. ref #27725
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    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.html
  • lines changed 46, context: html, text, full: html, text
    038d6e68ca59681d6cf608de90cfd7e1b8cb9c98 Thu Sep 9 17:30:45 2021 -0700
    adding MANE v 0.95
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
  • lines changed 18, context: html, text, full: html, text
    038d6e68ca59681d6cf608de90cfd7e1b8cb9c98 Thu Sep 9 17:30:45 2021 -0700
    adding MANE v 0.95
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    3e8fa8ff297998d1d7541ce2c30318cede07c839 Mon Sep 13 07:47:56 2021 -0700
    skip some fields on the hgc page for MANE
• src/hg/makeDb/trackDb/human/hg38/mane.html
  • lines changed 6, context: html, text, full: html, text
    d6f3e143147dc5af3509cf43b6ee6b180b808fc8 Thu Sep 9 15:24:19 2021 -0700
    Adding some more information on MANE, and linking to FAQ page refs #28132
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
  • lines changed 7, context: html, text, full: html, text
    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
  • lines changed 1, context: html, text, full: html, text
    e84cc337aa1d51342114f09b4bdb086fa83fd83d Wed Sep 8 13:40:09 2021 -0700
    Removed a set of parenthesis.
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
  • lines changed 8, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/oldKnownGene.ra
  • lines changed 8, context: html, text, full: html, text
    8dae6ccad320bbf99332a5b238cdda8c061c7d3d Tue Sep 7 16:50:41 2021 -0700
    add fast lookup for archived V36
  • lines changed 7, context: html, text, full: html, text
    6c71aade20591b09be29f6fa38e420c7f91ba18b Mon Sep 13 07:52:31 2021 -0700
    temporarily remove search rule for knownGene archive as it is interfering with the "real" track
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra
  • lines changed 8, context: html, text, full: html, text
    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/rectumWang.html
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    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/rectumWang.ra
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    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.html
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    475af5bc7ad6fcd3f691c863197c2ec25659d0d3 Wed Sep 8 13:23:41 2021 -0700
    Added Data Access section and links to subtracks. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra
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    361ea058a749423d3cf60e2408f4f876d4b811e5 Wed Sep 8 13:25:36 2021 -0700
    Added link to Cell Browser. refs #26965 #26969 #26973 #28059 #27727 #27724 #26970 #27725 #26968 #26966 #27726
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
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    0822a8d26540f2fd455b6088907351ba503e7346 Fri Sep 10 15:07:33 2021 -0700
    Adding pennant icon to trackDb.241way, refs #27519
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    c138b5ec2061de1ba8a4eeb89e49e53711265dee Wed Sep 8 11:13:40 2021 -0700
    Initial add of hg38 GTEx tracks. refs #27947
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    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
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    038d6e68ca59681d6cf608de90cfd7e1b8cb9c98 Thu Sep 9 17:30:45 2021 -0700
    adding MANE v 0.95
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    656a2699632b602bd1f6debe7cfdefa71094600f Fri Sep 10 14:16:37 2021 -0700
    Removing trackDb.241way release tags, refs #27519
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.dev.ra
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    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.new.ra
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    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
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    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
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    52f35889991c305a0bc9c0af47204e38f1c27c89 Wed Sep 8 17:33:39 2021 -0700
    Removing p12 patch pennantIcon as requested for folder icon addition refs #25035
• src/hg/makeDb/trackDb/human/trackDb.ra
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    4fc2a6702672293eb09e5a4c951b2f6d16257e5f Tue Sep 7 17:13:11 2021 -0700
    try to avoid the SNP disambiguation page on search results.
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    bcf2010d5334ef0a63b0bfd07f528380960988cb Fri Sep 10 16:32:42 2021 -0700
    add shortCircuit back to snpedia and gwasCatalog
• src/hg/makeDb/trackDb/mouse/trackDb.ra
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    4fc2a6702672293eb09e5a4c951b2f6d16257e5f Tue Sep 7 17:13:11 2021 -0700
    try to avoid the SNP disambiguation page on search results.
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    141e054d12c8225efd762bf56ccf6fb5179c738b Mon Sep 13 07:49:28 2021 -0700
    add bigGenePred to skipFields
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    4fc2a6702672293eb09e5a4c951b2f6d16257e5f Tue Sep 7 17:13:11 2021 -0700
    try to avoid the SNP disambiguation page on search results.
• src/hg/utils/otto/knownGene/buildCore.sh
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    e324c30e7ce5e418400c3123ac3343b58704f3f7 Sat Sep 11 07:28:28 2021 -0700
    ongoing work on knownGene V38
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    4efa4aebadc39cb64a256c3489035b00bd2abdc6 Wed Sep 8 12:06:50 2021 -0700
    Remove dependency on reference.fa from aligning new sequences; add tree-annotated Nextstrain clade and Pango lineage to metadata.
• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
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    2ae2c57f81bed91b2474771b896de8bc885b6b21 Wed Sep 8 12:04:46 2021 -0700
    Don't prepend country and append year if isolate name (e.g. from BioSample) already includes those.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    4efa4aebadc39cb64a256c3489035b00bd2abdc6 Wed Sep 8 12:06:50 2021 -0700
    Remove dependency on reference.fa from aligning new sequences; add tree-annotated Nextstrain clade and Pango lineage to metadata.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    39d3f511f6022a1b86ba79a68b19b3878e50db89 Wed Sep 8 12:07:05 2021 -0700
    New script for generating lineageTree.pb used by pangolin --usher: re-root big tree to lineage A, generate random-representative subtrees, test & pick least discordant tree.
• src/inc/basicBed.h
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    fefdc562bc014756f3c22f53dce16126ada37b56 Wed Sep 8 11:09:33 2021 -0700
    update bad blocks message to read as documentation refs #28131
• src/lib/basicBed.c
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    fefdc562bc014756f3c22f53dce16126ada37b56 Wed Sep 8 11:09:33 2021 -0700
    update bad blocks message to read as documentation refs #28131
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    74545feb9a7243db89d1007709287f657d78091b Wed Sep 8 15:14:33 2021 -0700
    changed error message when beginning of a block is not zero. documentation everywhere calls the 12th field blockStarts, though the code uses chromStarts
• src/product/installer/browserSetup.sh
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    37ab391fe381c15194bd46529e9508d9953a8a68 Mon Sep 13 07:55:52 2021 -0700
    fixing Gbic again for Centos8, because Fedora support broke centos8 support, refs #27795
• src/utils/hubPublicMail
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    0fb2d5e975296447fb73ba0bd702a0ac0414432e Fri Sep 10 07:46:27 2021 -0700
    Tweaking the help message to hubPublicMail, refs #27779
• src/utils/qa/weeklybld/buildEnv.csh
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    12911681c2aa0c7e44ddd7e0939eff52760860a9 Mon Sep 13 10:07:34 2021 -0700
    v421 preview1, refs #28041

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