All File Changes

v436_base to v437_preview (2022-08-29 to 2022-09-05) v437

• src/hca/hcaUnifyMatrix/makefile
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    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
• src/hca/hcaUnpack5/hcaUnpack5.c
  • lines changed 100, context: html, text, full: html, text
    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
• src/hca/hcaUnpack5/makefile
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    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
• src/hg/hgGateway/hgGateway.html
  • lines changed 1, context: html, text, full: html, text
    5a768ac3e29375e54bb9b05121e21f1d26ee87fe Fri Sep 2 13:06:54 2022 -0700
    Add a loading icon on hgGateway when a species is searched or a position is searched, refs #29765
• src/hg/hgTables/filterFields.c
  • lines changed 7, context: html, text, full: html, text
    8ceac2927ac2acf185674c484a2d95783782c058 Fri Sep 2 12:59:02 2022 -0700
    Improving documenation of Free-form query so users know that they need to enter correctly formatted SQL clause into the form. refs #rm29960
• src/hg/hgTrackUi/hgTrackUi.c
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    672d35a053738c40cd6fc026e1d10a109c102f37 Wed Aug 31 15:58:17 2022 -0700
    remove some of the multiwig options for sequence logo tracks
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    672d35a053738c40cd6fc026e1d10a109c102f37 Wed Aug 31 15:58:17 2022 -0700
    remove some of the multiwig options for sequence logo tracks
• src/hg/hgc/facetedBar.c
  • lines changed 12, context: html, text, full: html, text
    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
• src/hg/htdocs/goldenPath/help/cloud.html
  • lines changed 430, context: html, text, full: html, text
    98a9f12dcb9aac0ebf3aff6baa7351f0132bc60e Wed Aug 31 16:42:50 2022 -0700
    Adding Cloud help page for NAR paper (can be revamped as Data Access page) refs #28386
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 22, context: html, text, full: html, text
    2125538ce566450c32acefe3771d93c4857d1b2b Thu Sep 1 11:53:30 2022 -0700
    Updating news for Illumina Array tracks, refs #29309 #29492
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    fb4e67b847321757ce9e32fe2772681c694b1a01 Sun Sep 4 21:37:30 2022 -0700
    commenting out announcement of education content while I encode quotes and other chars not displaying correctly on RR
• src/hg/htdocs/images/phylo/hg38_470way.png
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    df75987a142e43b68e4a9a3e830de704ec4119b6 Tue Aug 30 14:07:52 2022 -0700
    a trimmed down phylo tree to represent the 470-way multiz refs #29898
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    98a9f12dcb9aac0ebf3aff6baa7351f0132bc60e Wed Aug 31 16:42:50 2022 -0700
    Adding Cloud help page for NAR paper (can be revamped as Data Access page) refs #28386
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    2125538ce566450c32acefe3771d93c4857d1b2b Thu Sep 1 11:53:30 2022 -0700
    Updating news for Illumina Array tracks, refs #29309 #29492
  • lines changed 14, context: html, text, full: html, text
    fb4e67b847321757ce9e32fe2772681c694b1a01 Sun Sep 4 21:37:30 2022 -0700
    commenting out announcement of education content while I encode quotes and other chars not displaying correctly on RR
• src/hg/htdocs/training/index.html
  • lines changed 13, context: html, text, full: html, text
    fb4e67b847321757ce9e32fe2772681c694b1a01 Sun Sep 4 21:37:30 2022 -0700
    commenting out announcement of education content while I encode quotes and other chars not displaying correctly on RR
• src/hg/js/autocompleteCat.js
  • lines changed 20, context: html, text, full: html, text
    5a768ac3e29375e54bb9b05121e21f1d26ee87fe Fri Sep 2 13:06:54 2022 -0700
    Add a loading icon on hgGateway when a species is searched or a position is searched, refs #29765
• src/hg/lib/hgncBig62.as
  • lines changed 54, context: html, text, full: html, text
    48578d7724625cda2499bd11f8b6ce19463a1279 Fri Sep 2 15:24:25 2022 -0700
    HGNC track is ready for QA.
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    672d35a053738c40cd6fc026e1d10a109c102f37 Wed Aug 31 15:58:17 2022 -0700
    remove some of the multiwig options for sequence logo tracks
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 74, context: html, text, full: html, text
    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
• src/hg/makeDb/doc/hg38/hgnc.txt
  • lines changed 29, context: html, text, full: html, text
    48578d7724625cda2499bd11f8b6ce19463a1279 Fri Sep 2 15:24:25 2022 -0700
    HGNC track is ready for QA.
• src/hg/makeDb/doc/hg38/multiz470way.txt
  • lines changed 179, context: html, text, full: html, text
    066250f183599972b357caf9d3261aad59451ad9 Mon Aug 29 16:19:11 2022 -0700
    with phyloP histogram refs #29898
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e72161af79bddd20fff3ed598df6c832d8794d50 Wed Aug 31 15:47:31 2022 -0700
    adding GCF_024166365.1_mEleMax1_primary_haplotype Asiatic elephant per user request refs #29905
• src/hg/makeDb/trackDb/human/genCC.html
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    984db3e3fb98fa5399455e929627ce72007531be Sun Sep 4 18:04:20 2022 -0700
    changed a word
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 23, context: html, text, full: html, text
    f61b03d465a0a853b932fce4bfaecba508f46318 Tue Aug 30 11:14:46 2022 -0700
    Code review edits to hg38/hg19 genotypeArrays.html, refs #29939
  • lines changed 1, context: html, text, full: html, text
    ad77f3239571ce2bf4743b7e2207aab83417973f Wed Aug 31 16:48:32 2022 -0700
    Fixed typo (positions) on the description page, refs #29309 #29492
  • lines changed 4, context: html, text, full: html, text
    521fa1323981e125e58666d89c5d194dc614dbcb Thu Sep 1 11:08:06 2022 -0700
    Updating Brookes email address on the description page refs #29309 #29492
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5a5d1ad05596cc213c5402e8dd3106d17cd593cb Mon Aug 29 10:57:19 2022 -0700
    Adding beta tags, #29309 #29492
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    7dcdbc72df0239a1b6d079eaf85a83442445bb2b Wed Aug 31 17:01:30 2022 -0700
    Removing release tags for the Illumina Array tracks, refs #29309 #29492
  • lines changed 1, context: html, text, full: html, text
    2125538ce566450c32acefe3771d93c4857d1b2b Thu Sep 1 11:53:30 2022 -0700
    Updating news for Illumina Array tracks, refs #29309 #29492
  • lines changed 1, context: html, text, full: html, text
    7dde11a2065df52b99621ae9ff186c5d2677c92e Fri Sep 2 09:34:37 2022 -0700
    Fixed typo (Probesets) in shortLabel, refs, #29309
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 31, context: html, text, full: html, text
    555f16b93255299cdc4fbecc0cf716a3c174a7b3 Fri Sep 2 15:56:15 2022 -0700
    add back in the phastCons discussion refs #29898
• src/hg/makeDb/trackDb/human/hg38/genotypeArrays.html
  • lines changed 2, context: html, text, full: html, text
    f61b03d465a0a853b932fce4bfaecba508f46318 Tue Aug 30 11:14:46 2022 -0700
    Code review edits to hg38/hg19 genotypeArrays.html, refs #29939
  • lines changed 1, context: html, text, full: html, text
    ad77f3239571ce2bf4743b7e2207aab83417973f Wed Aug 31 16:48:32 2022 -0700
    Fixed typo (positions) on the description page, refs #29309 #29492
• src/hg/makeDb/trackDb/human/hg38/gtexSingleCell.ra
  • lines changed 138, context: html, text, full: html, text
    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
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    1104a92a4a7a7c218d99de8ada8243d1ad794735 Wed Aug 31 17:17:45 2022 -0700
    Add link to cell browser on gtex single cell track item pages, refs #29954
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    64fd65a21364ec2f74e1cc2dfc7aa1945025cd85 Thu Sep 1 08:26:41 2022 -0700
    Fix missing release tag in gtex single cell track, refs build email
• src/hg/makeDb/trackDb/human/hg38/gtexSnAtlas.html
  • lines changed 152, context: html, text, full: html, text
    5e44468eb184fe6ac30d6355ef25c5df97b8d1ca Wed Aug 31 15:46:57 2022 -0700
    Forgot track description page, refs #29954
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 7, context: html, text, full: html, text
    6000ab290932e65b33e633d9a00f7145d8eb262e Wed Aug 31 10:40:19 2022 -0700
    47way now has phastCons and conserved elements and eliminate the useless subGroup2 settings refs #29898
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 25, context: html, text, full: html, text
    412e56d251198b35ebac351c15003f732a1ef764 Mon Aug 29 15:05:08 2022 -0700
    turning on the phyloP track refs #29898
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    e1ae7b4c4b7db85a6043b82abb2444023c506607 Tue Aug 30 14:13:24 2022 -0700
    adding treeImage to the 470-way track refs #29898
  • lines changed 51, context: html, text, full: html, text
    6000ab290932e65b33e633d9a00f7145d8eb262e Wed Aug 31 10:40:19 2022 -0700
    47way now has phastCons and conserved elements and eliminate the useless subGroup2 settings refs #29898
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    6ded634176b25a7e41e27cb6ec23d6ffb5820a10 Wed Aug 31 16:37:34 2022 -0700
    now with sequence logo display refs #29898
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5a5d1ad05596cc213c5402e8dd3106d17cd593cb Mon Aug 29 10:57:19 2022 -0700
    Adding beta tags, #29309 #29492
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    beb1d4107f59977c8b19a4b99b8ae77154b6b5a0 Mon Aug 29 13:19:21 2022 -0700
    Adding the noScoreFilter setting to remove scores from the hg38 hgc page, refs #29309
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    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
  • lines changed 1, context: html, text, full: html, text
    84c3108dd96eabd59184780448efd5a4410e148d Wed Aug 31 15:44:00 2022 -0700
    Woops forgot one line of a merge conflict
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    7dcdbc72df0239a1b6d079eaf85a83442445bb2b Wed Aug 31 17:01:30 2022 -0700
    Removing release tags for the Illumina Array tracks, refs #29309 #29492
  • lines changed 1, context: html, text, full: html, text
    2125538ce566450c32acefe3771d93c4857d1b2b Thu Sep 1 11:53:30 2022 -0700
    Updating news for Illumina Array tracks, refs #29309 #29492
  • lines changed 1, context: html, text, full: html, text
    7dde11a2065df52b99621ae9ff186c5d2677c92e Fri Sep 2 09:34:37 2022 -0700
    Fixed typo (Probesets) in shortLabel, refs, #29309
• src/hg/makeDb/trackDb/human/hgnc.html
  • lines changed 36, context: html, text, full: html, text
    48578d7724625cda2499bd11f8b6ce19463a1279 Fri Sep 2 15:24:25 2022 -0700
    HGNC track is ready for QA.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    48578d7724625cda2499bd11f8b6ce19463a1279 Fri Sep 2 15:24:25 2022 -0700
    HGNC track is ready for QA.
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    8b82dc0128e19f13b9d5c4c7cec31c83c4e4c6a3 Sun Sep 4 14:36:16 2022 -0700
    search for omimGene2 should still use the table
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    e1ae7b4c4b7db85a6043b82abb2444023c506607 Tue Aug 30 14:13:24 2022 -0700
    adding treeImage to the 470-way track refs #29898
• src/hg/ratStuff/mafCounts/mafCounts.c
  • lines changed 3, context: html, text, full: html, text
    4d7b22546a7eee42f93719f2cfda6fbe0c853807 Wed Aug 31 13:48:03 2022 -0700
    ignore blocks with no sequence
• src/hg/utils/makefile
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    e429e3f28edce0fdbc671c894018a10ede244501 Fri Sep 2 14:13:16 2022 -0700
    adding gencodeVersionForGenes for userApps no redmine
• src/hg/utils/otto/omim/buildOmimTracks.sh
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    60ff056e1f85059922a4cb8532a9c8d1a7a7218d Wed Aug 31 11:47:17 2022 -0700
    update OMiM otto process to use ncbiRefSeq
• src/hg/utils/otto/omim/doOmimGene2.sh
  • lines changed 16, context: html, text, full: html, text
    60ff056e1f85059922a4cb8532a9c8d1a7a7218d Wed Aug 31 11:47:17 2022 -0700
    update OMiM otto process to use ncbiRefSeq
• src/hg/utils/otto/omim/makefile
  • lines changed 1, context: html, text, full: html, text
    60ff056e1f85059922a4cb8532a9c8d1a7a7218d Wed Aug 31 11:47:17 2022 -0700
    update OMiM otto process to use ncbiRefSeq
• src/makefile
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    85e9fd5545cbcfb750efccbce5c94a5876f0bb86 Fri Sep 2 13:02:17 2022 -0700
    adding tabToTabDir and matrixToBarChartBed to the userApps no redmine
• src/tabFile/makefile
  • lines changed 9, context: html, text, full: html, text
    85e9fd5545cbcfb750efccbce5c94a5876f0bb86 Fri Sep 2 13:02:17 2022 -0700
    adding tabToTabDir and matrixToBarChartBed to the userApps no redmine
• src/userApps/fetchKentSource.sh
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    a501eafc4a27f33341d7051af9e158723bd136d0 Fri Sep 2 13:59:48 2022 -0700
    add src/tabFile to support building tabToTabDir no redmine
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    85e9fd5545cbcfb750efccbce5c94a5876f0bb86 Fri Sep 2 13:02:17 2022 -0700
    adding tabToTabDir and matrixToBarChartBed to the userApps no redmine
• src/utils/matrixClusterColumns/matrixClusterColumns.c
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    ab7847c47ac5507a7e126691bb78826ed4ba345d Mon Sep 13 16:34:47 2021 -0700
    Staging GTEx single nuclei gene expression track, refs #29954
• src/utils/qa/weeklybld/buildEnv.csh
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    5b2af56a49dca80a92c81d499dea82996bea154c Mon Sep 5 10:26:45 2022 -0700
    v437 preview1, refs #29878

• lines changed: 1633
• files changed: 65