All File Changes

v377_preview2 to v377_base (2019-01-28 to 2019-02-04) v377

• src/hg/cirm/cdw/cdwServeTagStorm/cdwServeTagStorm.c
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    593b7cae184ebbcc4ac826d364f112c5b1f7e7c8 Wed Jan 30 12:54:49 2019 -0800
    Fixing micro bug that leaves a stray line at end of tsv tagStorm representation.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 3, context: html, text, full: html, text
    964247defac7fc42f8b4862b8f774ba2c85042be Mon Jan 28 15:04:06 2019 -0800
    Widening pie charts so as to reduce truncation of labels. Changing download button on analysis/query page to say 'download all matching' for clarity.
  • lines changed 75, context: html, text, full: html, text
    219b0be0d8242e460b4b2af9f154212491ff0804 Wed Jan 30 11:38:13 2019 -0800
    Fixing merge conflicts
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 3, context: html, text, full: html, text
    964247defac7fc42f8b4862b8f774ba2c85042be Mon Jan 28 15:04:06 2019 -0800
    Widening pie charts so as to reduce truncation of labels. Changing download button on analysis/query page to say 'download all matching' for clarity.
  • lines changed 1, context: html, text, full: html, text
    50992d0943e66df777eaf937a20b024e92dbac79 Wed Jan 30 13:09:23 2019 -0800
    Adding more info to version.doc
• src/hg/cirm/gateway/htdocs/bestPractices.html
  • lines changed 1, context: html, text, full: html, text
    27b43a0d869f0ef954e53c143e9fa892f1082334 Fri Feb 1 15:35:59 2019 -0800
    Changing padded-deck to no-gutters class elsewhere in static pages. Tweaks to cescgOrg page to make pictures not overlap eachother or other text. Removing unnecessary height/width parameters for images. Changing headers to be same color as button in menubar. refs #22840 #22817
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 30, context: html, text, full: html, text
    27b43a0d869f0ef954e53c143e9fa892f1082334 Fri Feb 1 15:35:59 2019 -0800
    Changing padded-deck to no-gutters class elsewhere in static pages. Tweaks to cescgOrg page to make pictures not overlap eachother or other text. Removing unnecessary height/width parameters for images. Changing headers to be same color as button in menubar. refs #22840 #22817
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 68, context: html, text, full: html, text
    27b43a0d869f0ef954e53c143e9fa892f1082334 Fri Feb 1 15:35:59 2019 -0800
    Changing padded-deck to no-gutters class elsewhere in static pages. Tweaks to cescgOrg page to make pictures not overlap eachother or other text. Removing unnecessary height/width parameters for images. Changing headers to be same color as button in menubar. refs #22840 #22817
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 1, context: html, text, full: html, text
    27b43a0d869f0ef954e53c143e9fa892f1082334 Fri Feb 1 15:35:59 2019 -0800
    Changing padded-deck to no-gutters class elsewhere in static pages. Tweaks to cescgOrg page to make pictures not overlap eachother or other text. Removing unnecessary height/width parameters for images. Changing headers to be same color as button in menubar. refs #22840 #22817
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 3, context: html, text, full: html, text
    27b43a0d869f0ef954e53c143e9fa892f1082334 Fri Feb 1 15:35:59 2019 -0800
    Changing padded-deck to no-gutters class elsewhere in static pages. Tweaks to cescgOrg page to make pictures not overlap eachother or other text. Removing unnecessary height/width parameters for images. Changing headers to be same color as button in menubar. refs #22840 #22817
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 16, context: html, text, full: html, text
    27b43a0d869f0ef954e53c143e9fa892f1082334 Fri Feb 1 15:35:59 2019 -0800
    Changing padded-deck to no-gutters class elsewhere in static pages. Tweaks to cescgOrg page to make pictures not overlap eachother or other text. Removing unnecessary height/width parameters for images. Changing headers to be same color as button in menubar. refs #22840 #22817
• src/hg/hgGene/hgGeneData/Mouse/mm7/links.ra
  • lines changed 6, context: html, text, full: html, text
    a3d3f5433cf713e79372fc0163d841a966875bbd Thu Jan 31 10:11:32 2019 -0800
    removing exonPrimer links from mm7 and mm8, refs #15342
• src/hg/hgGene/hgGeneData/Mouse/mm8/links.ra
  • lines changed 6, context: html, text, full: html, text
    a3d3f5433cf713e79372fc0163d841a966875bbd Thu Jan 31 10:11:32 2019 -0800
    removing exonPrimer links from mm7 and mm8, refs #15342
• src/hg/hgLogin/hgLogin.c
  • lines changed 7, context: html, text, full: html, text
    0e7f2b9590af8c526238af8a414b004a20b09f4f Tue Jan 29 11:22:12 2019 -0800
    fix checking of length of user name after URL encoding refs #22867
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    86ffe17e1364d4e4385bfe0defe6192a608261f9 Tue Jan 29 16:30:59 2019 -0800
    a couple of tweaks to URL visibilities #18544
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    7559014e16a1413623d48a4107040cf3d781cbfb Fri Feb 1 09:37:54 2019 -0800
    a few tweaks in response to code review #22866
  • lines changed 4, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/hgTracks/lollipop.c
  • lines changed 138, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/hgTracks/makefile
  • lines changed 2, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    41285d4fbd9c3a3e4023d7680182f292d21e34a0 Tue Jan 29 05:01:22 2019 -0800
    finishing touches for the refseq/HGMD track, refs #22659
  • lines changed 1, context: html, text, full: html, text
    557843ecd649fa8222c713efd23fd9e471653784 Wed Jan 30 09:09:43 2019 -0800
    fixing a very obvious logic bug in sameTableOrHandler in hgc which I made myself and I have trouble believing that this has never been a problem before. refs #22838
  • lines changed 2, context: html, text, full: html, text
    400c756f8f81526ed6b2be191dd87fb7dddaf643 Fri Feb 1 10:57:01 2019 -0800
    do not work on a tdb that is a NULL pointer in matchTableOrHandler() refs #22881
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 5, context: html, text, full: html, text
    13cbe0cd504e003dddcc87e3e3030757ee0ce537 Tue Jan 29 05:56:23 2019 -0800
    tiny docs change for barChartBoxplot, no redmine
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 81, context: html, text, full: html, text
    4cba7821e52522400a9dc915bf4da3f4d5672af1 Mon Feb 4 06:11:43 2019 -0800
    a few changes to the genes faq, no redmine I think
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 3, context: html, text, full: html, text
    cdb8ceaa8d9e55436cb176c9af895c4efc78919e Mon Jan 28 12:13:04 2019 -0800
    Code review updates, changing anchors, wording, and line breaks #22862
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 26, context: html, text, full: html, text
    cdb8ceaa8d9e55436cb176c9af895c4efc78919e Mon Jan 28 12:13:04 2019 -0800
    Code review updates, changing anchors, wording, and line breaks #22862
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 7, context: html, text, full: html, text
    cdb8ceaa8d9e55436cb176c9af895c4efc78919e Mon Jan 28 12:13:04 2019 -0800
    Code review updates, changing anchors, wording, and line breaks #22862
• src/hg/htdocs/training/index.html
  • lines changed 34, context: html, text, full: html, text
    fcb7a263ee62d55dfff8b40e3a8aa7eaf70c2880 Wed Jan 30 09:50:50 2019 -0800
    dropping completed arizona and ucsf workshops. moving austria and greece into active list
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    dfdb7818c69d9fc7ce50da997384ad295b9814f7 Fri Feb 1 14:09:54 2019 -0800
    drop completed oregon workshop and add link for later for austria
• src/hg/hubApi/hubApi.c
  • lines changed 82, context: html, text, full: html, text
    17796a0436ab2b1f767d2e571739e2a0c8bdb6ed Mon Jan 28 11:19:07 2019 -0800
    compact the hubPublicJsonOutput() as it becomes more generic refs #18869
  • lines changed 72, context: html, text, full: html, text
    77f17523d1115eb2fb85eaf747a76db0c6328204 Mon Jan 28 14:05:59 2019 -0800
    ready to start listing other things refs #18869
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    bf7b450d396d8fe15d5198d3e4a55d8ac864e6b3 Mon Jan 28 14:55:21 2019 -0800
    now output genome list for any hub refs #18869
  • lines changed 131, context: html, text, full: html, text
    4cb561203efce23398fe8328be64e15dbb06e98d Tue Jan 29 15:22:55 2019 -0800
    now with /list/tracks function example refs #18869
• src/hg/hubApi/makefile
  • lines changed 2, context: html, text, full: html, text
    77f17523d1115eb2fb85eaf747a76db0c6328204 Mon Jan 28 14:05:59 2019 -0800
    ready to start listing other things refs #18869
• src/hg/hubApi/tests/expected.json.gz
  • lines changed 0, context: html, text, full: html, text
    d81224bc20f1c0d172c39c36d2bbe2065a8a2274 Mon Jan 28 14:10:37 2019 -0800
    adding first test refs #18869
• src/hg/hubApi/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    d81224bc20f1c0d172c39c36d2bbe2065a8a2274 Mon Jan 28 14:10:37 2019 -0800
    adding first test refs #18869
• src/hg/inc/hvGfx.h
  • lines changed 6, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    4563dcac2feca42b6cb92fd296b314b4e82c731f Mon Feb 4 09:55:41 2019 -0800
    New version number v377
• src/hg/lib/tablesTables.c
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    d5abc37b7df95525c088c01e435ea79fb203a79e Wed Jan 30 13:08:15 2019 -0800
    Adding count of unshown things in facets
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    41285d4fbd9c3a3e4023d7680182f292d21e34a0 Tue Jan 29 05:01:22 2019 -0800
    finishing touches for the refseq/HGMD track, refs #22659
• src/hg/makeDb/doc/hg38/gdc.txt
  • lines changed 42, context: html, text, full: html, text
    d0b4f8fcbcc77f6071f369ff2af209b54be6ad56 Wed Jan 30 15:07:55 2019 -0800
    initial work on GDC cancer track
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 7, context: html, text, full: html, text
    41285d4fbd9c3a3e4023d7680182f292d21e34a0 Tue Jan 29 05:01:22 2019 -0800
    finishing touches for the refseq/HGMD track, refs #22659
• src/hg/makeDb/genbank/etc/build-genbank
  • lines changed 24, context: html, text, full: html, text
    3c12d7dd551ad0540d0e9025db11019d3cc7122a Thu Jan 31 12:20:43 2019 -0800
    some genbank changes to otto-mate the process
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 5, context: html, text, full: html, text
    3c12d7dd551ad0540d0e9025db11019d3cc7122a Thu Jan 31 12:20:43 2019 -0800
    some genbank changes to otto-mate the process
• src/hg/makeDb/trackDb/bacteria/staAur2/aaCounts.ra
  • lines changed 1, context: html, text, full: html, text
    04f101fef2804c8262f593b5d4e2a4cc6b5ed75a Tue Jan 29 17:44:46 2019 -0800
    must have scoreFilter specified to make scoreFilterByRange work refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/cons369way.html
  • lines changed 1947, context: html, text, full: html, text
    ea3e5911994d95f20e8ee78344cf022b87ec2d6b Wed Jan 30 15:29:26 2019 -0800
    initial tables for description page refs #19937
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    99bb697538c4f9d867a0997046ca2d9af4e57d0c Wed Jan 30 15:55:49 2019 -0800
    now with NCBI assembly outlinks refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/protBlat0.ra
  • lines changed 1647, context: html, text, full: html, text
    16a3c155e59fd909d698be936e2e8b2a16683a45 Sat Feb 2 15:26:48 2019 -0800
    adding protein blat bigPsl display refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/protBlat1.ra
  • lines changed 1719, context: html, text, full: html, text
    16a3c155e59fd909d698be936e2e8b2a16683a45 Sat Feb 2 15:26:48 2019 -0800
    adding protein blat bigPsl display refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    16a3c155e59fd909d698be936e2e8b2a16683a45 Sat Feb 2 15:26:48 2019 -0800
    adding protein blat bigPsl display refs #19937
  • lines changed 3, context: html, text, full: html, text
    cc7e9e4e1b0b383a45a448ac1f1376608a2b9230 Sat Feb 2 15:28:11 2019 -0800
    no colorByStrand for genePred refs #19937
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 2, context: html, text, full: html, text
    1b32f52b0a72a04888b211fb742c657c063fd776 Mon Jan 28 11:53:48 2019 -0800
    Adding db= to links ref#22861
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 2, context: html, text, full: html, text
    1b32f52b0a72a04888b211fb742c657c063fd776 Mon Jan 28 11:53:48 2019 -0800
    Adding db= to links ref#22861
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 2, context: html, text, full: html, text
    f9ff9e8028c0713a9b66d4030c2f4bdda67e2bba Mon Jan 28 12:51:33 2019 -0800
    Change to updated. refs #22712
• src/hg/makeDb/trackDb/mouse/mm10/singleCell.html
  • lines changed 50, context: html, text, full: html, text
    48ccd6b0166c25675bbd8ee185075de0d9b9c217 Mon Jan 28 13:16:20 2019 -0800
    Making sure all lines in singleCell.html are less than 100 characters and updating double quotes to use the HTML reference, ref #21811
  • lines changed 24, context: html, text, full: html, text
    7b87fe8e9368717bfd66915c04d6921a20cde616 Mon Jan 28 13:31:02 2019 -0800
    Using the definition list HTML tags instead of <p> and <b> tags, refs #21811
  • lines changed 3, context: html, text, full: html, text
    a2d80b4130615998f6ea6013f55190db5ad90635 Mon Jan 28 13:43:28 2019 -0800
    Adding the <b> tags to make the each dataset term bold. The <dt> tag does not seem to bolding the term like on template.html, refs #21811
  • lines changed 1, context: html, text, full: html, text
    41285d4fbd9c3a3e4023d7680182f292d21e34a0 Tue Jan 29 05:01:22 2019 -0800
    finishing touches for the refseq/HGMD track, refs #22659
  • lines changed 6, context: html, text, full: html, text
    1cb264a396b019baf392faf149d16646385a6953 Tue Jan 29 09:20:53 2019 -0800
    Adding target=_blank to a URL and updating redirected links, refs #21811
  • lines changed 1, context: html, text, full: html, text
    3504f7390962a76358f0e84cc13c9cf58f58e982 Thu Jan 31 14:59:37 2019 -0800
    Removing a line break, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
  • lines changed 1915, context: html, text, full: html, text
    4cba7821e52522400a9dc915bf4da3f4d5672af1 Mon Feb 4 06:11:43 2019 -0800
    a few changes to the genes faq, no redmine I think
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    4cba7821e52522400a9dc915bf4da3f4d5672af1 Mon Feb 4 06:11:43 2019 -0800
    a few changes to the genes faq, no redmine I think
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.tabulamuris.ra
  • lines changed 1, context: html, text, full: html, text
    2f2910902605c79be9b656811448876f7610573a Mon Jan 28 12:32:22 2019 -0800
    Adding the singleCell html page to the Cell Expression subtrack, refs #21811
  • lines changed 1753, context: html, text, full: html, text
    4cba7821e52522400a9dc915bf4da3f4d5672af1 Mon Feb 4 06:11:43 2019 -0800
    a few changes to the genes faq, no redmine I think
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 31, context: html, text, full: html, text
    41285d4fbd9c3a3e4023d7680182f292d21e34a0 Tue Jan 29 05:01:22 2019 -0800
    finishing touches for the refseq/HGMD track, refs #22659
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 6, context: html, text, full: html, text
    41285d4fbd9c3a3e4023d7680182f292d21e34a0 Tue Jan 29 05:01:22 2019 -0800
    finishing touches for the refseq/HGMD track, refs #22659
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 6, context: html, text, full: html, text
    1fd2446a2c310839c8499af76d635d566fc0d01e Wed Jan 30 08:57:32 2019 -0800
    Updating redirected links for gasAcu1, uiLink cronjob.
• src/hg/makeDb/trackDb/stickleback/gasAcu1/phastConsElements8way.html
  • lines changed 5, context: html, text, full: html, text
    1fd2446a2c310839c8499af76d635d566fc0d01e Wed Jan 30 08:57:32 2019 -0800
    Updating redirected links for gasAcu1, uiLink cronjob.
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndSingles.html
  • lines changed 3, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/gold.html
  • lines changed 1, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 4, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/rhMap.html
  • lines changed 2, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/vegaGeneZfish.html
  • lines changed 5, context: html, text, full: html, text
    3850e84702e12b9cbdd8a402bfd94cdc64b8922c Thu Jan 31 09:53:01 2019 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/inc/srcVersion.h
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    4563dcac2feca42b6cb92fd296b314b4e82c731f Mon Feb 4 09:55:41 2019 -0800
    New version number v377
• src/inc/vGfx.h
  • lines changed 6, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/lib/memgfx.c
  • lines changed 1, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/lib/vGfxPrivate.h
  • lines changed 1, context: html, text, full: html, text
    a715f8ee926e405d684ba6891aef9ef7c6b28475 Fri Feb 1 16:41:47 2019 -0800
    circle primitive and a basic version of lollipops
• src/utils/qa/weeklybld/buildEnv.csh
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    d1a623d318d18c9136bc12d5aae95acf936d67ba Mon Feb 4 09:54:50 2019 -0800
    v377 final build, refs #NNNNN

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• files changed: 83