All File Changes

v414_base to v415_preview (2021-05-03 to 2021-05-10) v415

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    00f51da4d5f3cf0284adb7512df7bfab0a68fb39 Sun May 9 01:11:47 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 3, context: html, text, full: html, text
    3d5a9151f45ad34ed48141c46ff63a0f4b0c6587 Tue May 4 19:13:49 2021 -0700
    #27506 fix bug introduced with dynamic blat where unhelpful error message generated if a hub does not have blat
• src/hg/hgTables/mainPage.c
  • lines changed 45, context: html, text, full: html, text
    4a7a8a5cfc6cddef3873bdef663321bb4d78b5c5 Mon Apr 19 11:38:02 2021 -0700
    First cut Ana's UI recs for TB main page. refs #27408
  • lines changed 55, context: html, text, full: html, text
    e0e5b9a1895ba717a40da8d979c5d917189a02a1 Fri Apr 30 09:22:25 2021 -0700
    Second cut TF facelift, based on feedback from JK, Key features: 1) Short help messages in pop-ups on each step. 2) Remove step numbers and instead distinguish steps with styling 3) Save vertical space (keep 'get output' button above fold). refs #27408
  • lines changed 27, context: html, text, full: html, text
    1acb66337ae981cc319c5cf468e7246c7207b276 Fri Apr 30 09:32:43 2021 -0700
    Remove 'custom tracks' and 'track hubs' buttons as per JK request. No longer needed as they are in drop-down menu. refs #27408
  • lines changed 10, context: html, text, full: html, text
    db9c2b48fcc1de441ccb8acd182394f038e6833b Mon May 3 18:03:40 2021 -0700
    Polish TB intro paragraph text. refs #27408
  • lines changed 1, context: html, text, full: html, text
    9555f873ab597399fe692b0f9d670c238bbd0fba Mon May 3 18:05:57 2021 -0700
    Polish TB intro paragraph text. refs #27408
  • lines changed 25, context: html, text, full: html, text
    7c4930b32e0580573bfc0a8dc37e64e0d49b23db Wed May 5 19:54:45 2021 -0700
    Code cleanup. refs #27408
  • lines changed 8, context: html, text, full: html, text
    42960c4f41f87f9b6e956eee5cd2dfd4c9a51e8c Fri May 7 07:54:19 2021 -0700
    Response to input from reviewers. refs #27408
  • lines changed 2, context: html, text, full: html, text
    d5fc87f9de23720555c52e6f05ba37db6218f4ef Fri May 7 08:12:53 2021 -0700
    Minor format changes. refs #27408
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    3bc237f2fea899a81e6f06bacd111b1e2c8a1a71 Wed Apr 14 08:34:37 2021 -0700
    Adjust HTML to work with description summary on supertrack member track UI. refs #24948
• src/hg/hgTracks/wigTrack.c
  • lines changed 26, context: html, text, full: html, text
    5e55b76e29e2ac663dcfa4e288bd0caa701ab3da Mon May 3 13:36:12 2021 -0700
    adding mouseOverFunction trackDb variable and feature to turn off mouse over value display for averaged values refs #27457
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    b5d4627742fdcea042f2e1f5d3a7926791498d2f Mon May 3 15:25:38 2021 -0700
    Adding rn7 to the list of releases, refs #26682
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 13, context: html, text, full: html, text
    ec4aefd07bb4048983f3706065442deee40a93bf Tue May 4 09:23:38 2021 -0700
    Adding new assembly rn7 to credits.html, refs #26682
• src/hg/htdocs/goldenPath/help/covidBrowserIntro.html
  • lines changed 2, context: html, text, full: html, text
    15a68c43d81746a20b74ef8a33d2eba34b366e4a Wed Apr 21 13:54:43 2021 -0700
    Fixing type and adding credit line No RM
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 1100, context: html, text, full: html, text
    16710630ded9c6f2c0ad0aaad7ceec12e6a5bd06 Mon May 10 03:58:42 2021 -0700
    updates for the mirror manual, markdown and html page, refs #27390
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 4, context: html, text, full: html, text
    9d2cbd1da73a9200791c44a0034014903b5eaa43 Tue May 4 10:24:37 2021 -0700
    adding mouseOverFunction refs #27457
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 1, context: html, text, full: html, text
    2cbafaa7ef33b88d43bb4bc5854e63b867d19e16 Mon May 3 16:08:28 2021 -0700
    Adding a anchor tag on trackDbHub for vcf, pointed out missing in code review refs #27446
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    5087ca698c04eee0bdc6d2766f8d5576272bb820 Fri Apr 30 14:41:41 2021 -0700
    Typo fix for cr http://redmine.soe.ucsc.edu/issues/27446
  • lines changed 11, context: html, text, full: html, text
    9d2cbd1da73a9200791c44a0034014903b5eaa43 Tue May 4 10:24:37 2021 -0700
    adding mouseOverFunction refs #27457
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 45, context: html, text, full: html, text
    399fb1f2827a004bac5e046c70a2ad02df19270f Tue May 4 11:21:39 2021 -0700
    Adding new assembly rn7 to newsArch page, refs #26682
• src/hg/htdocs/images/singleCell/liver-fig10.jpg
  • lines changed 0, context: html, text, full: html, text
    7017d6dc8b2cd864b9a6269dfebd14466f48df0e Wed May 5 15:11:14 2021 -0700
    Adding images for figures 3a, 3b, and 10 from paper for liverMacparland. refs #26970
• src/hg/htdocs/images/singleCell/liver-fig3a.jpg
  • lines changed 0, context: html, text, full: html, text
    7017d6dc8b2cd864b9a6269dfebd14466f48df0e Wed May 5 15:11:14 2021 -0700
    Adding images for figures 3a, 3b, and 10 from paper for liverMacparland. refs #26970
• src/hg/htdocs/images/singleCell/liver-fig3b.jpg
  • lines changed 0, context: html, text, full: html, text
    7017d6dc8b2cd864b9a6269dfebd14466f48df0e Wed May 5 15:11:14 2021 -0700
    Adding images for figures 3a, 3b, and 10 from paper for liverMacparland. refs #26970
• src/hg/htdocs/images/singleCell/muscle-fig1b.jpg
  • lines changed 0, context: html, text, full: html, text
    49e1d3dc9400ff650dc2260c72cf5ffe482f7cc1 Wed Apr 28 17:42:25 2021 -0700
    Adding image for figure 1b from paper for muscleDeMicheli track. refs #26968
• src/hg/htdocs/index.html
  • lines changed 4, context: html, text, full: html, text
    db437ffe81923ea8bda725b5cc50babac7463030 Wed May 5 03:06:59 2021 -0700
    more work on the license, refs #27498
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    783ca071b2a12b058d6330a6fd52bece470c77e1 Tue May 4 11:26:46 2021 -0700
    Adding new assembly rn7 to indexNews page, refs #26682
• src/hg/htdocs/license/index.html
  • lines changed 20, context: html, text, full: html, text
    3178e5e5af0c19f930e289b4d884de41b3170541 Tue May 4 01:42:52 2021 -0700
    making license page more obvious, refs #27498
  • lines changed 72, context: html, text, full: html, text
    503a6b5796e93aed92e899063b63db9b335bf91d Tue May 4 15:06:02 2021 -0700
    Improving license page refs #27391, #27415
• src/hg/htdocs/style/HGStyle.css
  • lines changed 25, context: html, text, full: html, text
    e0e5b9a1895ba717a40da8d979c5d917189a02a1 Fri Apr 30 09:22:25 2021 -0700
    Second cut TF facelift, based on feedback from JK, Key features: 1) Short help messages in pop-ups on each step. 2) Remove step numbers and instead distinguish steps with styling 3) Save vertical space (keep 'get output' button above fold). refs #27408
  • lines changed 17, context: html, text, full: html, text
    3984f5a01e24a3cb3ffd1063aa77014a2b29dfb0 Wed May 5 19:54:06 2021 -0700
    Code cleanup. refs #27408
  • lines changed 2, context: html, text, full: html, text
    8942da8fe90ccb4321fba12248ff22f571de0efa Fri May 7 02:17:01 2021 -0700
    changes after code review, refs #27488
• src/hg/htdocs/training/index.html
  • lines changed 20, context: html, text, full: html, text
    345c01767954625e4cb016ec932b1829a3a2003a Mon May 3 15:41:51 2021 -0700
    updating training sched, sadly all virtual
  • lines changed 1, context: html, text, full: html, text
    d6a044c78442ce5c1b82eb4163588bf88a32c558 Mon May 3 16:09:33 2021 -0700
    forgot to close an anchor tag
• src/hg/js/hgTracks.js
  • lines changed 13, context: html, text, full: html, text
    5e55b76e29e2ac663dcfa4e288bd0caa701ab3da Mon May 3 13:36:12 2021 -0700
    adding mouseOverFunction trackDb variable and feature to turn off mouse over value display for averaged values refs #27457
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    21a68d65206abc508c6400214aea8da6bc22b339 Wed May 5 15:51:28 2021 -0700
    Fix some hgTracks back button problems by disable web browser caching of CGI responses, refs #26627
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    b9d3e953e1cea321da23a6898442ea0b08954c54 Mon May 3 14:32:59 2021 -0700
    check for null hubStatus in trackHub structure
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    8c3d74369118f9b19b7befdfbf596bb0ae9b3ab5 Fri May 7 16:32:20 2021 -0700
    when passing coordinates to binKeeper, make sure the range is at least a base wide. This allows for zero width ranges to be lifted over. #24836
• src/hg/makeDb/doc/transMapTracks.txt
  • lines changed 6, context: html, text, full: html, text
    25cb79b4a110974de7622bc22f4970dbd9cf36b6 Tue May 4 18:36:51 2021 -0700
    added instructions for making transMap QA data
• src/hg/makeDb/trackDb/human/cadd.ra
  • lines changed 1, context: html, text, full: html, text
    5e55b76e29e2ac663dcfa4e288bd0caa701ab3da Mon May 3 13:36:12 2021 -0700
    adding mouseOverFunction trackDb variable and feature to turn off mouse over value display for averaged values refs #27457
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 2, context: html, text, full: html, text
    b837a5ce7897133870e5b1406f851f33514e984a Mon May 3 17:41:59 2021 -0700
    Collapsing to one mouse label for mm39 and mm10 Placental Chain/Net matrix, refs #18071
• src/hg/makeDb/trackDb/human/hg19/exomeProbesets.ra
  • lines changed 30, context: html, text, full: html, text
    c6f55ceb4ba3de1d914c08a167a19f7f40e76a7f Fri May 7 13:52:35 2021 -0700
    Fixing plus signs that caused errors refs #27515
• src/hg/makeDb/trackDb/human/hg19/gnomadPext.html
  • lines changed 2, context: html, text, full: html, text
    dee5a3c06a878f43eb3006f4c28ebf0ac935279a Sun May 9 12:55:17 2021 -0700
    grammar adjustment
• src/hg/makeDb/trackDb/human/hg38/exomeProbesets.ra
  • lines changed 26, context: html, text, full: html, text
    c6f55ceb4ba3de1d914c08a167a19f7f40e76a7f Fri May 7 13:52:35 2021 -0700
    Fixing plus signs that caused errors refs #27515
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    612dcaed090f39f1c36a96c8921e0e2712a64e01 Tue May 4 14:07:05 2021 -0700
    knownGene fast search should be the last short circuit search
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
  • lines changed 85, context: html, text, full: html, text
    3bc237f2fea899a81e6f06bacd111b1e2c8a1a71 Wed Apr 14 08:34:37 2021 -0700
    Adjust HTML to work with description summary on supertrack member track UI. refs #24948
• src/hg/makeDb/trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    332788bc3ec5f996faf44ead144df5b82ef1dc21 Mon May 3 16:16:59 2021 -0700
    Add relatedTracks table construction to beta and public makefile targets, refs #25721
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 5, context: html, text, full: html, text
    5e55b76e29e2ac663dcfa4e288bd0caa701ab3da Mon May 3 13:36:12 2021 -0700
    adding mouseOverFunction trackDb variable and feature to turn off mouse over value display for averaged values refs #27457
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 65, context: html, text, full: html, text
    24c443b10b97e5b1e81df9ee5cb393131e7b873a Wed May 5 11:40:43 2021 -0700
    better handling of assembly hub chain net tracks refs #26988
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
  • lines changed 126, context: html, text, full: html, text
    24c443b10b97e5b1e81df9ee5cb393131e7b873a Wed May 5 11:40:43 2021 -0700
    better handling of assembly hub chain net tracks refs #26988
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 21, context: html, text, full: html, text
    24c443b10b97e5b1e81df9ee5cb393131e7b873a Wed May 5 11:40:43 2021 -0700
    better handling of assembly hub chain net tracks refs #26988
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 40, context: html, text, full: html, text
    24c443b10b97e5b1e81df9ee5cb393131e7b873a Wed May 5 11:40:43 2021 -0700
    better handling of assembly hub chain net tracks refs #26988
• src/hg/utils/automation/pairLastz.sh
  • lines changed 13, context: html, text, full: html, text
    24c443b10b97e5b1e81df9ee5cb393131e7b873a Wed May 5 11:40:43 2021 -0700
    better handling of assembly hub chain net tracks refs #26988
• src/product/mirrorManual.txt
  • lines changed 427, context: html, text, full: html, text
    16710630ded9c6f2c0ad0aaad7ceec12e6a5bd06 Mon May 10 03:58:42 2021 -0700
    updates for the mirror manual, markdown and html page, refs #27390
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    7ef831eb18a26e507d90798a6a949ed46b3ff717 Mon May 10 10:02:42 2021 -0700
    v415 preview1, refs #27418

• lines changed: 2433
• files changed: 55