All File Changes

v402_preview to v402_preview2 (2020-07-20 to 2020-07-27) v402

• src/hg/hgTracks/bigBedTrack.c
  • lines changed 67, context: html, text, full: html, text
    66330ff4742dfc3b8f924017caf1c6419907bbbf Sat Jul 25 11:16:24 2020 -0700
    make merged Gencode filters much more similar to old style
• src/hg/hgTracks/gtexTracks.c
  • lines changed 2, context: html, text, full: html, text
    7c3b34b1f68877584541e8c0806caf609e923cc8 Sat Jul 25 12:49:32 2020 -0700
    get gtex to work with known databases
• src/hg/hgTracks/hgTracks.c
  • lines changed 46, context: html, text, full: html, text
    48de4e2ccfe829cfea8c38d9f1034aa217b04cf1 Mon Jul 20 10:57:49 2020 -0700
    Revert "fixing PDF output for new highlight cart variable format, also fixes a related problem that just came up on the ML, refs #25887" This reverts commit fb06bed25a9f45eaef8a875f3efbd45cfc14e804.
  • lines changed 36, context: html, text, full: html, text
    350733c85caaaebfe5c82892e57a38d60e70c1c3 Mon Jul 20 11:23:01 2020 -0700
    fixing a previous commit that I had reverted, refs #25887. Code review note: ignore the original commit and its reverted cousin This is the only relevant commit.
  • lines changed 9, context: html, text, full: html, text
    ee211bfbeedc99ca157c71ba3ba04ae6346b263b Tue Jul 21 02:11:14 2020 -0700
    support the super old chrom:start-end syntax again (found by Jonathan), adding back possibility to have higlights on two different dbs by removing check for db-prefix in hgTracks (the db-filtering is done by the javascript code anyways) and clean up the code a little by introducing a function that creates the highlight string from the parts instead of copied code. refs #21384
  • lines changed 189, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/hgTracks/hgTracks.h
  • lines changed 9, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/hgTracks/mainMain.c
  • lines changed 3, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/hgTracks/menu.c
  • lines changed 13, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/hgTracks/recTrackSets.c
  • lines changed 128, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/hgc/gtexClick.c
  • lines changed 2, context: html, text, full: html, text
    7c3b34b1f68877584541e8c0806caf609e923cc8 Sat Jul 25 12:49:32 2020 -0700
    get gtex to work with known databases
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 5, context: html, text, full: html, text
    347cd39dde8e7bac935c2858e2418601a9baf5a9 Mon Jul 20 13:58:52 2020 -0700
    Adding back a plug to the blog to #download36 refs #25775
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 127, context: html, text, full: html, text
    57ea2b9e93735c2cff66d3f4bd66d024636c7b83 Fri Jul 24 11:33:51 2020 -0700
    RefSeq Diff track set refs #22586
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/htdocs/inc/recommendedTrackSets.tab
  • lines changed 11, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    57ea2b9e93735c2cff66d3f4bd66d024636c7b83 Fri Jul 24 11:33:51 2020 -0700
    RefSeq Diff track set refs #22586
• src/hg/htdocs/style/HGStyle.css
  • lines changed 24, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    ee211bfbeedc99ca157c71ba3ba04ae6346b263b Tue Jul 21 02:11:14 2020 -0700
    support the super old chrom:start-end syntax again (found by Jonathan), adding back possibility to have higlights on two different dbs by removing check for db-prefix in hgTracks (the db-filtering is done by the javascript code anyways) and clean up the code a little by introducing a function that creates the highlight string from the parts instead of copied code. refs #21384
  • lines changed 42, context: html, text, full: html, text
    fc3472e7e9978eb81e3ac14e985bf27e5196ab73 Fri Jul 24 10:58:01 2020 -0700
    Recommended track sets feature. refs #25601
• src/hg/js/utils.js
  • lines changed 13, context: html, text, full: html, text
    ee211bfbeedc99ca157c71ba3ba04ae6346b263b Tue Jul 21 02:11:14 2020 -0700
    support the super old chrom:start-end syntax again (found by Jonathan), adding back possibility to have higlights on two different dbs by removing check for db-prefix in hgTracks (the db-filtering is done by the javascript code anyways) and clean up the code a little by introducing a function that creates the highlight string from the parts instead of copied code. refs #21384
• src/hg/lib/hui.c
  • lines changed 37, context: html, text, full: html, text
    66330ff4742dfc3b8f924017caf1c6419907bbbf Sat Jul 25 11:16:24 2020 -0700
    make merged Gencode filters much more similar to old style
• src/hg/lib/trackDbCache.c
  • lines changed 1, context: html, text, full: html, text
    84df75d080e0b29596c6d2cc9b96df9212e49415 Fri Jul 24 12:15:31 2020 -0700
    make the trackDbCache dir writable by other
• src/hg/logCrawl/dbTrackAndSearchUsage/makefile
  • lines changed 5, context: html, text, full: html, text
    401352088c5776094516da2b9f617ae5a1357bad Mon Jul 20 15:14:28 2020 -0700
    Adding apache error log trimmer used to make counting database and track usage faster and easier
• src/hg/logCrawl/dbTrackAndSearchUsage/trimTrackLogs
  • lines changed 111, context: html, text, full: html, text
    401352088c5776094516da2b9f617ae5a1357bad Mon Jul 20 15:14:28 2020 -0700
    Adding apache error log trimmer used to make counting database and track usage faster and easier
  • lines changed 4, context: html, text, full: html, text
    b01e95110f02879f2c581743c81655b1011fb350 Tue Jul 21 16:52:34 2020 -0700
    Fix bug in error log trimmer when munging two lines together
• src/hg/makeDb/doc/wuhCor1/contacts.txt
  • lines changed 2, context: html, text, full: html, text
    700f17522f59d037cffe5a6f5a505eb313a965a3 Tue Jul 21 05:16:28 2020 -0700
    adding makedocs and fixes to track docs for contact wuhCor1 tracks, refs #25910
• src/hg/makeDb/doc/wuhCor1/icshape.txt
  • lines changed 6, context: html, text, full: html, text
    bd7a05523fb883ccaa2fa7cce4e380522105c3a0 Thu Jul 23 01:40:46 2020 -0700
    adding icshape wuhCor1 track, refs #25942
• src/hg/makeDb/doc/wuhCor1/phyloGenes.txt
  • lines changed 2, context: html, text, full: html, text
    11dcee554fb49f7631db7d34371ff9a241943ab1 Fri Jul 24 02:21:30 2020 -0700
    adding phyloCsf genes to wuhCor1, refs #25946
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 85, context: html, text, full: html, text
    237e07884cbbc8b2f4a9b4d030f782372ed61892 Mon Jul 20 16:20:26 2020 -0700
    Adding Problematic Sites track for SARS-CoV-2. refs #25916
  • lines changed 13, context: html, text, full: html, text
    fd2962e7e75b86f8a231fc382609eb567bc6b906 Wed Jul 22 14:44:34 2020 -0700
    Replacing Rob's tree with a collapsed (mutation nodes only) version from Yatish. refs #25904
  • lines changed 10, context: html, text, full: html, text
    d98829260a7890c9bc05a55bc8cba2e1a31a533f Fri Jul 24 10:04:21 2020 -0700
    Added instructions for downloading metadata (including lineage assignments) from GISAID/EpiCoV. refs #25904
• src/hg/makeDb/doc/wuhCor1/pond.txt
  • lines changed 1, context: html, text, full: html, text
    6667aa55ce0d46a79d174f04288e78660a4f1b60 Fri Jul 24 06:29:58 2020 -0700
    adding natural selection (pond) track to wuhCor1, refs #25947
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 1, context: html, text, full: html, text
    f052d1d18ea9b1505ef33525620e58a3153104e5 Tue Jul 21 13:54:00 2020 -0700
    reworded a sentence
• src/hg/makeDb/trackDb/human/hg38/gencodeV35.ra
  • lines changed 3, context: html, text, full: html, text
    66330ff4742dfc3b8f924017caf1c6419907bbbf Sat Jul 25 11:16:24 2020 -0700
    make merged Gencode filters much more similar to old style
  • lines changed 16, context: html, text, full: html, text
    eccc7de60949e4623f9196e39d48c6e009c74b6b Sat Jul 25 11:28:49 2020 -0700
    put GENCODE V35 first, stop including knownGene
• src/hg/makeDb/trackDb/human/hg38/tgpTrios.html
  • lines changed 8, context: html, text, full: html, text
    5a953e59bb13c4600a1ce455cb2d97370451e106 Mon Jul 20 15:48:39 2020 -0700
    Code review #25920
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    948fb3ba7766cae2d51e8acc6eecbd055b012876 Tue Jul 21 15:30:57 2020 -0700
    Releasing trios track to the RR #25582
  • lines changed 1, context: html, text, full: html, text
    eccc7de60949e4623f9196e39d48c6e009c74b6b Sat Jul 25 11:28:49 2020 -0700
    put GENCODE V35 first, stop including knownGene
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 37, context: html, text, full: html, text
    e7c53e49485ab14146a43157c4eba77bda38e7e0 Fri Jul 24 16:11:34 2020 -0700
    Work in progress combination of the clingen dosage tracks
• src/hg/makeDb/trackDb/virus/wuhCor1/contacts.html
  • lines changed 22, context: html, text, full: html, text
    ec91666fb5afb7d8d6410fa2be4da5aaca2f8505 Tue Jul 21 05:04:05 2020 -0700
    adding wuhCor1 contacts track docs page, refs #25910
  • lines changed 6, context: html, text, full: html, text
    700f17522f59d037cffe5a6f5a505eb313a965a3 Tue Jul 21 05:16:28 2020 -0700
    adding makedocs and fixes to track docs for contact wuhCor1 tracks, refs #25910
  • lines changed 5, context: html, text, full: html, text
    71d44a6ae7734144cfbe0fb42f06483ed023f401 Wed Jul 22 06:12:10 2020 -0700
    updating contacts track on wuhCor1, refs #25910
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html
  • lines changed 4, context: html, text, full: html, text
    eb5f18f57a1a4486c0d3031ab24e5711e4d625d8 Fri Jul 17 16:55:10 2020 -0700
    Adding examples for the Data Access section, refs #25481
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainParsimony.html
  • lines changed 5, context: html, text, full: html, text
    3a74688594914299a2ae8ecc42e68325d04df709 Fri Jul 24 11:08:48 2020 -0700
    Final edit to parsimony track #25799
• src/hg/makeDb/trackDb/virus/wuhCor1/phyloGenes.html
  • lines changed 24, context: html, text, full: html, text
    11dcee554fb49f7631db7d34371ff9a241943ab1 Fri Jul 24 02:21:30 2020 -0700
    adding phyloCsf genes to wuhCor1, refs #25946
  • lines changed 0, context: html, text, full: html, text
    9c8d34bb08cf622ee058537ff3680a3f04775145 Fri Jul 24 05:02:21 2020 -0700
    fixing msdos line endings in track docs file, found by nightly build, refs #25946
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.html
  • lines changed 39, context: html, text, full: html, text
    6667aa55ce0d46a79d174f04288e78660a4f1b60 Fri Jul 24 06:29:58 2020 -0700
    adding natural selection (pond) track to wuhCor1, refs #25947
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.ra
  • lines changed 108, context: html, text, full: html, text
    6667aa55ce0d46a79d174f04288e78660a4f1b60 Fri Jul 24 06:29:58 2020 -0700
    adding natural selection (pond) track to wuhCor1, refs #25947
• src/hg/makeDb/trackDb/virus/wuhCor1/problematicSites.html
  • lines changed 100, context: html, text, full: html, text
    237e07884cbbc8b2f4a9b4d030f782372ed61892 Mon Jul 20 16:20:26 2020 -0700
    Adding Problematic Sites track for SARS-CoV-2. refs #25916
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html
  • lines changed 21, context: html, text, full: html, text
    1928113a8dc1d0a242e722696dbb0c36b6e983c0 Mon Jul 20 10:54:11 2020 -0700
    Add references that reflect UCSC's work on identifying problematic sites to SARS-CoV-2 Phylogeny details (thx David). refs #25904
  • lines changed 2, context: html, text, full: html, text
    3b0f4d47a5037c5bda659d15f665e08b152d302b Mon Jul 20 16:47:53 2020 -0700
    Removing API line and shortening longLabel refs #25904
  • lines changed 2, context: html, text, full: html, text
    c555bcc38d7a963aef36a8aa7a321d125cda0b87 Tue Jul 21 15:31:25 2020 -0700
    Modifying html to reflect max left label width #25904
  • lines changed 10, context: html, text, full: html, text
    fd2962e7e75b86f8a231fc382609eb567bc6b906 Wed Jul 22 14:44:34 2020 -0700
    Replacing Rob's tree with a collapsed (mutation nodes only) version from Yatish. refs #25904
  • lines changed 64, context: html, text, full: html, text
    711cb4fa97618deb2b2f1f92c56ba08e72efec5a Wed Jul 22 17:23:17 2020 -0700
    Added lineage coloring key as requested by David. refs #25904
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 1, context: html, text, full: html, text
    ed0005bde8db6c4e36e51654f79ad1a9365edc72 Tue Jul 21 11:58:49 2020 -0700
    Hiding nextstrain #25904
  • lines changed 1, context: html, text, full: html, text
    3a74688594914299a2ae8ecc42e68325d04df709 Fri Jul 24 11:08:48 2020 -0700
    Final edit to parsimony track #25799
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1928113a8dc1d0a242e722696dbb0c36b6e983c0 Mon Jul 20 10:54:11 2020 -0700
    Add references that reflect UCSC's work on identifying problematic sites to SARS-CoV-2 Phylogeny details (thx David). refs #25904
  • lines changed 30, context: html, text, full: html, text
    237e07884cbbc8b2f4a9b4d030f782372ed61892 Mon Jul 20 16:20:26 2020 -0700
    Adding Problematic Sites track for SARS-CoV-2. refs #25916
  • lines changed 1, context: html, text, full: html, text
    3b0f4d47a5037c5bda659d15f665e08b152d302b Mon Jul 20 16:47:53 2020 -0700
    Removing API line and shortening longLabel refs #25904
  • lines changed 4, context: html, text, full: html, text
    e4d666d58e3c798400104bb556327705f2b0ee41 Tue Jul 21 11:38:35 2020 -0700
    Releasing Phylo track #25904
  • lines changed 1, context: html, text, full: html, text
    71d44a6ae7734144cfbe0fb42f06483ed023f401 Wed Jul 22 06:12:10 2020 -0700
    updating contacts track on wuhCor1, refs #25910
  • lines changed 32, context: html, text, full: html, text
    bd7a05523fb883ccaa2fa7cce4e380522105c3a0 Thu Jul 23 01:40:46 2020 -0700
    adding icshape wuhCor1 track, refs #25942
  • lines changed 33, context: html, text, full: html, text
    11dcee554fb49f7631db7d34371ff9a241943ab1 Fri Jul 24 02:21:30 2020 -0700
    adding phyloCsf genes to wuhCor1, refs #25946
  • lines changed 1, context: html, text, full: html, text
    6667aa55ce0d46a79d174f04288e78660a4f1b60 Fri Jul 24 06:29:58 2020 -0700
    adding natural selection (pond) track to wuhCor1, refs #25947
• src/hg/makeDb/trackDb/zebrafish/danRer5/affyConsensusAndTargetZonWildType.html
  • lines changed 1, context: html, text, full: html, text
    20bd661d434984530e5828bc6fa2e9e68e2a175a Tue Jul 21 10:39:45 2020 -0700
    Updating redirected links found by the uiLinks cronjob, no redmine.
• src/hg/near/hgNear/hgNearData/Human/hg38/genome.ra
  • lines changed 3, context: html, text, full: html, text
    b4028e02a32b0e2d61115f8c48085e10db618573 Sat Jul 25 13:16:38 2020 -0700
    add externalDb to hg38 hgNearData
• src/hg/utils/hubCheck/tests/input/araTha1.trackDb.txt
  • lines changed 4, context: html, text, full: html, text
    1bd844ab30d579e45193fc40b8089607259464c8 Mon Jul 27 09:54:10 2020 -0700
    Removing test dependency on third party hub provider so nightly build doesn't break
• src/hg/utils/otto/lovd/checkAndLoad.sh
  • lines changed 53, context: html, text, full: html, text
    81ed6a428f3655d2f32f1cc523993632955e2e6f Fri Jul 24 17:04:40 2020 -0700
    Fix up LOVD otto script after code review, refs #25925
• src/hg/utils/otto/lovd/download.sh
  • lines changed 16, context: html, text, full: html, text
    81ed6a428f3655d2f32f1cc523993632955e2e6f Fri Jul 24 17:04:40 2020 -0700
    Fix up LOVD otto script after code review, refs #25925
• src/utils/qa/weeklybld/buildEnv.csh
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    05da1a2f544cfcfe07b4849f27f9e60b73c4937d Mon Jul 27 10:01:21 2020 -0700
    v402 preview2

• lines changed: 1692
• files changed: 71