All File Changes

v407_preview to v407_preview2 (2020-11-02 to 2020-11-09) v407

• src/hg/hgGene/hgGene.c
  • lines changed 19, context: html, text, full: html, text
    199af1bfc7e950026d4392777113e6bf6d8d61f9 Mon Nov 9 03:27:48 2020 -0800
    libifying refseq summary abbreviator and also running on the refGene hgc page. refs #26454
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 7, context: html, text, full: html, text
    3816f803ab7502f867eae1f3424fdf0dfa7a64e7 Fri Nov 6 02:47:01 2020 -0800
    removing link to Stanford SOURCE, refs #26452
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ef8bc9f4cd18895278dfcf68a073a18e240bc90c Mon Nov 9 01:33:43 2020 -0800
    Tiny change to hgTracks help text, refs #26490
• src/hg/hgTracks/lollyTrack.c
  • lines changed 30, context: html, text, full: html, text
    a6a236e1f1855cb202d1824435bdf797cf07ad47 Mon Nov 2 16:24:47 2020 -0800
    add support for bigLolly custom tracks and specifying lolly trackDb fields that specify a field using the name of the field OR the field number
  • lines changed 2, context: html, text, full: html, text
    a3191890642f8b6e4fd76b4605c12f87c0f2b019 Wed Nov 4 14:54:17 2020 -0800
    some tweaks to make bigLolly axes work better
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    265965d20e4498d2e9639f0099d6e777d7612f35 Tue Nov 3 03:01:13 2020 -0800
    adding a small comment to a source code file, no redmine
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    4390310b0fa270367bc7b18e5728bfb1a2a9670d Mon Nov 2 16:05:32 2020 -0800
    mouse over popup now has a one second delay before appearing refs #21980
  • lines changed 3, context: html, text, full: html, text
    914829451ce180351f7822e72d4cdb25a9d8221e Tue Nov 3 09:43:39 2020 -0800
    back to the hidden div method of transmitting jsonData is present refs #21980
  • lines changed 6, context: html, text, full: html, text
    5fef9ecfe121867dc6bd750a6a01b46150bb868e Tue Nov 3 15:46:21 2020 -0800
    dirty checkin for transition to click through to description page working and streamline the popUp text window definition refs #21980
  • lines changed 1, context: html, text, full: html, text
    2681b20edd79e1a1416c474da922f9c01898c7cc Fri Nov 6 10:24:19 2020 -0800
    turn mouse overs off for rm26491 patch refs #26491
  • lines changed 16, context: html, text, full: html, text
    7d425214dcf40fa365f6f448379b709ec071eab4 Fri Nov 6 22:43:17 2020 -0800
    now showing mean of values when not at base display refs #21980
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    a6a236e1f1855cb202d1824435bdf797cf07ad47 Mon Nov 2 16:24:47 2020 -0800
    add support for bigLolly custom tracks and specifying lolly trackDb fields that specify a field using the name of the field OR the field number
  • lines changed 2, context: html, text, full: html, text
    199af1bfc7e950026d4392777113e6bf6d8d61f9 Mon Nov 9 03:27:48 2020 -0800
    libifying refseq summary abbreviator and also running on the refGene hgc page. refs #26454
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 5, context: html, text, full: html, text
    5ce838669ec36aedcf37a394a3067a2190af2a50 Tue Nov 3 06:28:49 2020 -0800
    reverse bigBarChart order of bars on hgc page, refs #26461
• src/hg/hgc/mafClick.c
  • lines changed 25, context: html, text, full: html, text
    0bbf348b54a73fedf15ee0c53cf3f4e109eaf9c1 Tue Nov 3 15:53:19 2020 -0800
    fix infinite loop error that happens if speciesOrder has reference species in it.
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 22, context: html, text, full: html, text
    1586330213411f03154ec815ec9addb9d4656329 Mon Nov 9 07:43:10 2020 -0800
    improving readability of NCBI versus refGene section, refs #26496
• src/hg/htdocs/covid19.html
  • lines changed 18, context: html, text, full: html, text
    67255df25296381bdd716c760d255eb45c984bab Wed Nov 4 10:25:43 2020 -0800
    Adding links to news on covid19 and changing some links based on htmlCheck checkLink
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 55, context: html, text, full: html, text
    a6a236e1f1855cb202d1824435bdf797cf07ad47 Mon Nov 2 16:24:47 2020 -0800
    add support for bigLolly custom tracks and specifying lolly trackDb fields that specify a field using the name of the field OR the field number
  • lines changed 8, context: html, text, full: html, text
    a88a7c5da243a1a94d3dd3637aec21110a6167d1 Wed Nov 4 14:53:17 2020 -0800
    working on bigLolly doc
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 68, context: html, text, full: html, text
    545ec79f2978a465c7ac581f7ee1a7e60021cff3 Tue Nov 3 15:40:33 2020 -0800
    Fixing up the viewing section for refs #26462
  • lines changed 0, context: html, text, full: html, text
    7acca9312bae40a7e3dc2ec867fc3e9db4cb06d5 Tue Nov 3 16:18:04 2020 -0800
    Fixing quick typo #26462
  • lines changed 2, context: html, text, full: html, text
    54ee780bf3ce0daf8148978766d4c7cfccba8b0d Tue Nov 3 16:19:03 2020 -0800
    Fixing quick typo #26462
  • lines changed 43, context: html, text, full: html, text
    be3d8b28bd4ee8c75dec5878957b7650ed8f066b Wed Nov 4 12:31:16 2020 -0800
    Emphasizing sessions for sharing hubs #26462
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    a88a7c5da243a1a94d3dd3637aec21110a6167d1 Wed Nov 4 14:53:17 2020 -0800
    working on bigLolly doc
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 5, context: html, text, full: html, text
    a88a7c5da243a1a94d3dd3637aec21110a6167d1 Wed Nov 4 14:53:17 2020 -0800
    working on bigLolly doc
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    a88a7c5da243a1a94d3dd3637aec21110a6167d1 Wed Nov 4 14:53:17 2020 -0800
    working on bigLolly doc
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 28, context: html, text, full: html, text
    5f1a2569a3778e610356fc24fd8ead95a031c157 Mon Nov 2 17:11:31 2020 -0800
    dded the pennantIcon, hid the Mean proportion tracks, and drafted announcement HTML pages, and added to the gnomAD super track page refs #25869
  • lines changed 2, context: html, text, full: html, text
    eb0604fa0969fb042aa54b96d638d4114931d755 Tue Nov 3 14:20:25 2020 -0800
    Slight wording change for announcement #25869
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 2, context: html, text, full: html, text
    d0ec3559b70a8a4dd7e6ae2c7f000591a72f1571 Thu Nov 5 15:38:07 2020 -0800
    replaced mm9 with mm39 on the gemomes menu refs #26397
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 2, context: html, text, full: html, text
    d0ec3559b70a8a4dd7e6ae2c7f000591a72f1571 Thu Nov 5 15:38:07 2020 -0800
    replaced mm9 with mm39 on the gemomes menu refs #26397
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    5f1a2569a3778e610356fc24fd8ead95a031c157 Mon Nov 2 17:11:31 2020 -0800
    dded the pennantIcon, hid the Mean proportion tracks, and drafted announcement HTML pages, and added to the gnomAD super track page refs #25869
• src/hg/htdocs/style/mouseOver.css
  • lines changed 20, context: html, text, full: html, text
    5fef9ecfe121867dc6bd750a6a01b46150bb868e Tue Nov 3 15:46:21 2020 -0800
    dirty checkin for transition to click through to description page working and streamline the popUp text window definition refs #21980
  • lines changed 33, context: html, text, full: html, text
    b461f5b5a9ce1d6232f662b08b5900e3161cf971 Wed Nov 4 11:22:29 2020 -0800
    cleaned up mouseOver.css refs #21980
  • lines changed 10, context: html, text, full: html, text
    a7f78f08720da04dad7ca9c490d8fca072678a31 Fri Nov 6 16:30:37 2020 -0800
    vertical line is now three dark light dark so it shows up on any background refs #21980
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    199af1bfc7e950026d4392777113e6bf6d8d61f9 Mon Nov 9 03:27:48 2020 -0800
    libifying refseq summary abbreviator and also running on the refGene hgc page. refs #26454
• src/hg/js/hgTracks.js
  • lines changed 45, context: html, text, full: html, text
    4390310b0fa270367bc7b18e5728bfb1a2a9670d Mon Nov 2 16:05:32 2020 -0800
    mouse over popup now has a one second delay before appearing refs #21980
  • lines changed 15, context: html, text, full: html, text
    914829451ce180351f7822e72d4cdb25a9d8221e Tue Nov 3 09:43:39 2020 -0800
    back to the hidden div method of transmitting jsonData is present refs #21980
  • lines changed 68, context: html, text, full: html, text
    5fef9ecfe121867dc6bd750a6a01b46150bb868e Tue Nov 3 15:46:21 2020 -0800
    dirty checkin for transition to click through to description page working and streamline the popUp text window definition refs #21980
  • lines changed 74, context: html, text, full: html, text
    34df9e8eb07f50c8508992991190fbb8642ac070 Tue Nov 3 16:02:40 2020 -0800
    remove debug garbage and obsolete code, there is an off by one or two X position error refs #21980
  • lines changed 40, context: html, text, full: html, text
    48a9ad0dffa17597791e51ac5dbaf38eee270864 Wed Nov 4 11:18:44 2020 -0800
    clean up mouseOver.css and fix off positions in hgTracks refs #21980
  • lines changed 46, context: html, text, full: html, text
    d323d8fed58ef2bcb55fc137b4d2ac312ea87c37 Wed Nov 4 16:45:22 2020 -0800
    I was lost, and now I've been found refs #21980
  • lines changed 25, context: html, text, full: html, text
    ccd08d555773febb9d221bb3be960651503de0d0 Wed Nov 4 22:48:16 2020 -0800
    now working correctly on Firefox, Chrome, Safari and Edge refs #21980
  • lines changed 36, context: html, text, full: html, text
    1f4bdbe42a9a575812cd8de8419ed7a951a24e1c Fri Nov 6 16:41:56 2020 -0800
    centered the message text and might now recognize when tracks turn on when they were silent refs #21980
  • lines changed 3, context: html, text, full: html, text
    f3e4bf4342a01d96c1da56e07faacdf2e194a50f Fri Nov 6 16:53:14 2020 -0800
    apply the magic 3 to the left offsets for vertical line and message box refs #21980
  • lines changed 4, context: html, text, full: html, text
    41722bb9ef37f7742c9e493b748f59920c0d90df Fri Nov 6 22:39:39 2020 -0800
    now showing mean of values when not at base display refs #21980
• src/hg/js/subCfg.js
  • lines changed 10, context: html, text, full: html, text
    ebd1bc7d12458534c826eb6a6b0170518dddc9a9 Fri Nov 6 14:38:42 2020 -0800
    subCfg.js if id missing just use name instead.
• src/hg/lib/customFactory.c
  • lines changed 18, context: html, text, full: html, text
    a6a236e1f1855cb202d1824435bdf797cf07ad47 Mon Nov 2 16:24:47 2020 -0800
    add support for bigLolly custom tracks and specifying lolly trackDb fields that specify a field using the name of the field OR the field number
• src/hg/lib/hdb.c
  • lines changed 23, context: html, text, full: html, text
    199af1bfc7e950026d4392777113e6bf6d8d61f9 Mon Nov 9 03:27:48 2020 -0800
    libifying refseq summary abbreviator and also running on the refGene hgc page. refs #26454
• src/hg/makeDb/doc/wuhCor1/pyle.txt
  • lines changed 1, context: html, text, full: html, text
    0d7048029043241fa317d1289cd5c8a99ce694a7 Wed Nov 4 06:11:12 2020 -0800
    adding wuhCor1 pyle rna structure track refs #26466
• src/hg/makeDb/doc/wuhCor1/treangen.txt
  • lines changed 1, context: html, text, full: html, text
    0d7048029043241fa317d1289cd5c8a99ce694a7 Wed Nov 4 06:11:12 2020 -0800
    adding wuhCor1 pyle rna structure track refs #26466
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    6cc335cac480981d4082ca982354d8881ef4636c Fri Nov 6 15:51:11 2020 -0800
    Adding neoSch1 to beta genbank updates refs #19883
• src/hg/makeDb/trackDb/human/covidHgeMuts.html
  • lines changed 73, context: html, text, full: html, text
    18806024b9a6a9e1cc1d2211467705ec9227c7e8 Thu Nov 5 10:49:14 2020 -0800
    added table to desc page refs #26351
• src/hg/makeDb/trackDb/human/covidMuts.html
  • lines changed 119, context: html, text, full: html, text
    c8294a0f61de291ccf0eb848363768c1d502a2f6 Fri Nov 6 05:09:43 2020 -0800
    tables added to desc page #26351
• src/hg/makeDb/trackDb/human/giab.html
  • lines changed 3, context: html, text, full: html, text
    98296985b0763ebf2d6add3b51d9200ac6940d77 Thu Nov 5 06:21:39 2020 -0800
    added variant regions in track description refs #24349
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 3, context: html, text, full: html, text
    5f1a2569a3778e610356fc24fd8ead95a031c157 Mon Nov 2 17:11:31 2020 -0800
    dded the pennantIcon, hid the Mean proportion tracks, and drafted announcement HTML pages, and added to the gnomAD super track page refs #25869
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    5056b2bf397b278092513018dd4e6c24aa195777 Mon Nov 2 15:56:21 2020 -0800
    Hiding Mean Coverage tracks refs #25869
  • lines changed 2, context: html, text, full: html, text
    5f1a2569a3778e610356fc24fd8ead95a031c157 Mon Nov 2 17:11:31 2020 -0800
    dded the pennantIcon, hid the Mean proportion tracks, and drafted announcement HTML pages, and added to the gnomAD super track page refs #25869
  • lines changed 26, context: html, text, full: html, text
    72353c31ac345c3dada82bf581d1567f874c06a2 Tue Nov 3 12:08:09 2020 -0800
    Adding gnomAD v2.1.1 whole genome vcf to bigBed track, refs #25010
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 4, context: html, text, full: html, text
    aa40ce7e05f8258122f9ce48f6eb08c8dff942fb Tue Nov 3 16:20:53 2020 -0800
    Updating default track and switching priority to show gtex v8 refs #25130
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSFpower.html
  • lines changed 1, context: html, text, full: html, text
    f3ef057cf30099d59de48902fd252bafb01b2f23 Fri Nov 6 10:07:48 2020 -0800
    updating redirected links for wuhCor1 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra
  • lines changed 1, context: html, text, full: html, text
    f6caaa06772b844d6a731351768be90455ece560 Wed Nov 4 06:17:08 2020 -0800
    fixing small type in wuhCor1 trackDb, no redmine
  • lines changed 2, context: html, text, full: html, text
    f2b37f114ad33663dad2026eb2440aa51f1a8e02 Wed Nov 4 06:20:33 2020 -0800
    fixing wuhCor1 trackDb typos, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/microdel.html
  • lines changed 1, context: html, text, full: html, text
    f3ef057cf30099d59de48902fd252bafb01b2f23 Fri Nov 6 10:07:48 2020 -0800
    updating redirected links for wuhCor1 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/virus/wuhCor1/minkMuts.html
  • lines changed 1, context: html, text, full: html, text
    0526056ccce5073e3a75d6257c7462f3368af803 Mon Nov 9 06:39:11 2020 -0800
    adding the mink mutations and antibody escape tracks for wuhCor1, refs #26497
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.ra
  • lines changed 71, context: html, text, full: html, text
    d4e8b74dd2b8b443590219b31938c52926026a41 Mon Nov 2 10:26:50 2020 -0800
    remove unreferenced file
• src/hg/makeDb/trackDb/virus/wuhCor1/phyloGenes.html
  • lines changed 1, context: html, text, full: html, text
    f3ef057cf30099d59de48902fd252bafb01b2f23 Fri Nov 6 10:07:48 2020 -0800
    updating redirected links for wuhCor1 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/virus/wuhCor1/pyle.html
  • lines changed 47, context: html, text, full: html, text
    0d7048029043241fa317d1289cd5c8a99ce694a7 Wed Nov 4 06:11:12 2020 -0800
    adding wuhCor1 pyle rna structure track refs #26466
  • lines changed 21, context: html, text, full: html, text
    a8a28f782bce387fc7a0281b9a64893fe765be26 Thu Nov 5 09:13:23 2020 -0800
    Quick QA for wuhCor1 track refs #26466
• src/hg/makeDb/trackDb/virus/wuhCor1/pyle.ra
  • lines changed 26, context: html, text, full: html, text
    f2b37f114ad33663dad2026eb2440aa51f1a8e02 Wed Nov 4 06:20:33 2020 -0800
    fixing wuhCor1 trackDb typos, no redmine
  • lines changed 1, context: html, text, full: html, text
    a8a28f782bce387fc7a0281b9a64893fe765be26 Thu Nov 5 09:13:23 2020 -0800
    Quick QA for wuhCor1 track refs #26466
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    0d7048029043241fa317d1289cd5c8a99ce694a7 Wed Nov 4 06:11:12 2020 -0800
    adding wuhCor1 pyle rna structure track refs #26466
  • lines changed 17, context: html, text, full: html, text
    0526056ccce5073e3a75d6257c7462f3368af803 Mon Nov 9 06:39:11 2020 -0800
    adding the mink mutations and antibody escape tracks for wuhCor1, refs #26497
• src/hg/makeDb/trackDb/virus/wuhCor1/treangen.html
  • lines changed 33, context: html, text, full: html, text
    1bc2e64b4571836b0a6fceed917239b4df4d2e67 Wed Nov 4 06:12:28 2020 -0800
    adding wuhCor1 intrahost variants track, refs #26465
  • lines changed 18, context: html, text, full: html, text
    2d9bdb9df82a573e06bd0079809838a10f12e199 Wed Nov 4 15:31:09 2020 -0800
    Quick QA for wuhCor1 track refs #26465
• src/hg/makeDb/trackDb/virus/wuhCor1/treangen.ra
  • lines changed 8, context: html, text, full: html, text
    0d7048029043241fa317d1289cd5c8a99ce694a7 Wed Nov 4 06:11:12 2020 -0800
    adding wuhCor1 pyle rna structure track refs #26466
  • lines changed 1, context: html, text, full: html, text
    2d9bdb9df82a573e06bd0079809838a10f12e199 Wed Nov 4 15:31:09 2020 -0800
    Quick QA for wuhCor1 track refs #26465
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 6, context: html, text, full: html, text
    0ce9210dc769e64e79daf51e11ab0f08774c287f Mon Nov 9 05:12:43 2020 -0800
    making clinvar otto a little bit less verbose, no redmine
• src/lib/cheapcgi.c
  • lines changed 4, context: html, text, full: html, text
    b204f93e26319c81615e1a1f5d68b2aa2de0865f Thu Nov 5 22:45:40 2020 -0800
    Added support for id in hidden shadow for cgiMakeCheckBox. fixes #26467
• src/utils/bigHeat
  • lines changed 181, context: html, text, full: html, text
    1a1b94ac3518c1b9dfdf08f25605e505cf14f359 Fri Nov 6 07:38:57 2020 -0800
    adding bigHeat helper script inspired by Hiram's email, no redmine
• src/utils/makefile
  • lines changed 3, context: html, text, full: html, text
    1a1b94ac3518c1b9dfdf08f25605e505cf14f359 Fri Nov 6 07:38:57 2020 -0800
    adding bigHeat helper script inspired by Hiram's email, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    83846b0d3b7508f17bf61cbd4614c6bb9f9c50eb Mon Nov 9 09:55:27 2020 -0800
    v407 preview2

• lines changed: 1555
• files changed: 81