All File Changes

v406_preview2 to v406_base (2020-10-19 to 2020-10-26) v406

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    98c00541ab52088a538da6ace320aa49b4789fe3 Sun Oct 25 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    98c00541ab52088a538da6ace320aa49b4789fe3 Sun Oct 25 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    98c00541ab52088a538da6ace320aa49b4789fe3 Sun Oct 25 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    76e7bac242cc25e1dbcbb9f9d16dc1be01ed6519 Thu Oct 22 21:10:33 2020 -0700
    comment out mouseOver business until later refs #21980
• src/hg/hgTracks/lollyTrack.c
  • lines changed 4, context: html, text, full: html, text
    d807b60fd721c00051ac7e7cf5088eedba7170eb Thu Oct 22 13:28:01 2020 -0700
    in response to code review
• src/hg/hgTracks/vcfTrack.c
  • lines changed 5, context: html, text, full: html, text
    358232fdd2fe9b78248b54fd38a9cd2f52ff4586 Wed Oct 21 12:49:05 2020 -0700
    lineFileUdcMayOpen automatically decompresses local files but not urls. netLineFileMayOpen does automatically decompress. For now, just use netLineFileMayOpen, although in the long term it would be better to ad support to lineFileUdcMayOpen to get the benefits of caching.
• src/hg/hgTracks/wigTrack.c
  • lines changed 32, context: html, text, full: html, text
    f309250d6d5934baf893f66405952d1f91f98ffe Thu Oct 22 16:00:02 2020 -0700
    feature is still off but has been improved with json data sent to the client refs #21980
  • lines changed 13, context: html, text, full: html, text
    581e1380e193c49cf80d3e29630d4cd27f2cd186 Thu Oct 22 16:06:56 2020 -0700
    only output the mouseOver element once refs #21980
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 0, context: html, text, full: html, text
    d807b60fd721c00051ac7e7cf5088eedba7170eb Thu Oct 22 13:28:01 2020 -0700
    in response to code review
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 3, context: html, text, full: html, text
    217f4cc528e07dbc39ac2be950c64f048da78c30 Thu Oct 15 12:07:12 2020 -0700
    Fixing broken outlink refs #9677
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
  • lines changed 1, context: html, text, full: html, text
    4224a8c96b5c03ed1dc6069e9d80a30aaabcaeee Thu Oct 22 01:38:04 2020 -0700
    Fixing minor URL issue, no ticket
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 26, context: html, text, full: html, text
    207d69212eab2b97857769bff4e886c393817db5 Thu Oct 22 01:41:34 2020 -0700
    Documentation for trackDb settings that change the default parameters of a hic track, refs #26312
  • lines changed 5, context: html, text, full: html, text
    43d0ad2887d6554d8a5478cda9a145e142ff1d68 Thu Oct 22 02:23:26 2020 -0700
    Adding anchors to a few new trackDb settings, refs #26312
  • lines changed 2, context: html, text, full: html, text
    e95480c10bf8352b320f2cd209fdbb53750765ca Fri Oct 23 15:48:47 2020 -0700
    Revising autoScale documentation after advice, refs #26312
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 21, context: html, text, full: html, text
    207d69212eab2b97857769bff4e886c393817db5 Thu Oct 22 01:41:34 2020 -0700
    Documentation for trackDb settings that change the default parameters of a hic track, refs #26312
  • lines changed 5, context: html, text, full: html, text
    43d0ad2887d6554d8a5478cda9a145e142ff1d68 Thu Oct 22 02:23:26 2020 -0700
    Adding anchors to a few new trackDb settings, refs #26312
  • lines changed 2, context: html, text, full: html, text
    e95480c10bf8352b320f2cd209fdbb53750765ca Fri Oct 23 15:48:47 2020 -0700
    Revising autoScale documentation after advice, refs #26312
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 66, context: html, text, full: html, text
    207d69212eab2b97857769bff4e886c393817db5 Thu Oct 22 01:41:34 2020 -0700
    Documentation for trackDb settings that change the default parameters of a hic track, refs #26312
  • lines changed 37, context: html, text, full: html, text
    e95480c10bf8352b320f2cd209fdbb53750765ca Fri Oct 23 15:48:47 2020 -0700
    Revising autoScale documentation after advice, refs #26312
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 147, context: html, text, full: html, text
    8627f085aa0d1397dea24329d08cd243a13e39ef Tue Oct 20 16:05:44 2020 -0700
    4th coronavirus release announcement refs #26280
  • lines changed 44, context: html, text, full: html, text
    489979945330d4839dc0cb1c0631189ef8687381 Fri Oct 23 11:58:06 2020 -0700
    Announcing the mm39 assembly, refs #22271
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    8627f085aa0d1397dea24329d08cd243a13e39ef Tue Oct 20 16:05:44 2020 -0700
    4th coronavirus release announcement refs #26280
  • lines changed 12, context: html, text, full: html, text
    489979945330d4839dc0cb1c0631189ef8687381 Fri Oct 23 11:58:06 2020 -0700
    Announcing the mm39 assembly, refs #22271
• src/hg/htdocs/style/mouseOver.css
  • lines changed 30, context: html, text, full: html, text
    d811c26cd8f8e0e196de1672e43763d48e2f5b72 Thu Oct 22 15:51:24 2020 -0700
    initial crufty version refs #21980
• src/hg/inc/hicUi.h
  • lines changed 10, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    126705aca26f380da73ae4c8998bd64edd09118c Mon Oct 26 10:01:47 2020 -0700
    New version number v406
• src/hg/js/hui.js
  • lines changed 12, context: html, text, full: html, text
    feb380e4c526092d9793e1d70f8a484cca2ae338 Tue Oct 20 01:18:28 2020 -0700
    Fix speed of javascript in View, Facets, and Subtracks for hgTrackUi. fixes #26381
  • lines changed 2, context: html, text, full: html, text
    580bf7de78a35e5d3fbbdc8171ffcf80a795f877 Thu Oct 22 19:46:56 2020 -0700
    Fix speed of javascript in Matrix for hgTrackUi. fixes #26398
  • lines changed 3, context: html, text, full: html, text
    e8aeb1dcada5968de429029c2496185abae6f8f1 Fri Oct 23 02:26:23 2020 -0700
    Handle single-dimension matrix in hui.c, and handle missing g track tag in hui.js. refs #26398
• src/hg/js/mouseOver.js
  • lines changed 157, context: html, text, full: html, text
    95abbde729e668386b62b8fb6a254493d30edfc2 Thu Oct 22 15:29:48 2020 -0700
    initial dirty version of mouseOver on wiggles refs #21980
  • lines changed 59, context: html, text, full: html, text
    06c7ed413236324b8633cbbf66d5569dc0dbf71f Thu Oct 22 15:50:04 2020 -0700
    removed cruft for a clean version refs #21980
• src/hg/js/subCfg.js
  • lines changed 2, context: html, text, full: html, text
    feb380e4c526092d9793e1d70f8a484cca2ae338 Tue Oct 20 01:18:28 2020 -0700
    Fix speed of javascript in View, Facets, and Subtracks for hgTrackUi. fixes #26381
• src/hg/js/utils.js
  • lines changed 9, context: html, text, full: html, text
    feb380e4c526092d9793e1d70f8a484cca2ae338 Tue Oct 20 01:18:28 2020 -0700
    Fix speed of javascript in View, Facets, and Subtracks for hgTrackUi. fixes #26381
• src/hg/lib/customTrack.c
  • lines changed 1, context: html, text, full: html, text
    98d6fb247a79e7a09337fdfb0bbdaaa6e4b3e0ba Fri Oct 23 15:53:01 2020 -0700
    Fixing color=0,0,0 being ignored for hic tracks, refs #26312
• src/hg/lib/googleAnalytics.c
  • lines changed 1, context: html, text, full: html, text
    d8bf76ed7e182223d91aa19c9655438974b9c8c0 Wed Oct 14 09:22:15 2020 -0700
    adding outbound link tracking to hgGene, refs #21916
• src/hg/lib/hicUi.c
  • lines changed 58, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
• src/hg/lib/hui.c
  • lines changed 23, context: html, text, full: html, text
    feb380e4c526092d9793e1d70f8a484cca2ae338 Tue Oct 20 01:18:28 2020 -0700
    Fix speed of javascript in View, Facets, and Subtracks for hgTrackUi. fixes #26381
  • lines changed 30, context: html, text, full: html, text
    580bf7de78a35e5d3fbbdc8171ffcf80a795f877 Thu Oct 22 19:46:56 2020 -0700
    Fix speed of javascript in Matrix for hgTrackUi. fixes #26398
  • lines changed 13, context: html, text, full: html, text
    e8aeb1dcada5968de429029c2496185abae6f8f1 Fri Oct 23 02:26:23 2020 -0700
    Handle single-dimension matrix in hui.c, and handle missing g track tag in hui.js. refs #26398
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 5, context: html, text, full: html, text
    bdb0cd1324dd7f96ab40203b2c9a031e9bd9d0cf Wed Oct 21 12:55:37 2020 -0700
    Adding note for next time about how a file mysteriously ended up with garbage at the end.
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 11, context: html, text, full: html, text
    22d0df7a78276cdebe8cf0cc5f46cc0498e78738 Tue Oct 20 01:06:12 2020 -0700
    added reference to desc page #26330
• src/hg/makeDb/trackDb/human/clinvarSubLolly.html
  • lines changed 1, context: html, text, full: html, text
    fec384d549572b9e03a61b5ade92512889c8b003 Thu Oct 22 13:05:53 2020 -0700
    remove clinvarSubLolly specific HTML file
• src/hg/makeDb/trackDb/human/covidHgeMuts.html
  • lines changed 7, context: html, text, full: html, text
    863141dcd6a4651b3b4f1644d95a4b364b4265be Mon Oct 26 00:41:22 2020 -0700
    corrected spelling suggestions refs #26372
• src/hg/makeDb/trackDb/human/giab.html
  • lines changed 22, context: html, text, full: html, text
    0bcf60137c26f30375bb9f03edd6da8354fdf26c Fri Oct 23 16:53:34 2020 -0700
    Making each line less than 100 characters. Updated a link to the multi-view docs to use the relative path. refs #24349 #25873
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 41, context: html, text, full: html, text
    b85c91f713cb5886b6f630db993d0eb3cb15b504 Fri Oct 23 12:48:37 2020 -0700
    included gnomAD FAQ link and improved references
• src/hg/makeDb/trackDb/human/hg19/gnomadCoverage.html
  • lines changed 42, context: html, text, full: html, text
    b85c91f713cb5886b6f630db993d0eb3cb15b504 Fri Oct 23 12:48:37 2020 -0700
    included gnomAD FAQ link and improved references
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 40, context: html, text, full: html, text
    b85c91f713cb5886b6f630db993d0eb3cb15b504 Fri Oct 23 12:48:37 2020 -0700
    included gnomAD FAQ link and improved references
• src/hg/makeDb/trackDb/human/hg19/gnomadPext.html
  • lines changed 51, context: html, text, full: html, text
    b85c91f713cb5886b6f630db993d0eb3cb15b504 Fri Oct 23 12:48:37 2020 -0700
    included gnomAD FAQ link and improved references
  • lines changed 3, context: html, text, full: html, text
    92b12b9dc7533de32816e43f9aae5d762ce7f91e Mon Oct 26 00:34:00 2020 -0700
    added Anna and Chris to Credits refs #26372
• src/hg/makeDb/trackDb/human/hg19/gnomadSv.html
  • lines changed 45, context: html, text, full: html, text
    b85c91f713cb5886b6f630db993d0eb3cb15b504 Fri Oct 23 12:48:37 2020 -0700
    included gnomAD FAQ link and improved references
• src/hg/makeDb/trackDb/human/hg19/gnomadVariants.html
  • lines changed 42, context: html, text, full: html, text
    b85c91f713cb5886b6f630db993d0eb3cb15b504 Fri Oct 23 12:48:37 2020 -0700
    included gnomAD FAQ link and improved references
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 19, context: html, text, full: html, text
    eb91bdbd593e04364d969b7461c1f690325da0e5 Tue Oct 20 16:39:13 2020 -0700
    Fix bug in ref/alt name shortening in vcfToBed, refs #25010
  • lines changed 79, context: html, text, full: html, text
    d29df3e746be393237adb4df980d9c1a9f489898 Fri Oct 23 12:45:54 2020 -0700
    improved track labels hypens and underscores refs #26372
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 8, context: html, text, full: html, text
    d807b60fd721c00051ac7e7cf5088eedba7170eb Thu Oct 22 13:28:01 2020 -0700
    in response to code review
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 4, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
  • lines changed 2, context: html, text, full: html, text
    d807b60fd721c00051ac7e7cf5088eedba7170eb Thu Oct 22 13:28:01 2020 -0700
    in response to code review
• src/hg/makeDb/trackDb/virus/wuhCor1/iedb.html
  • lines changed 27, context: html, text, full: html, text
    9d0ca15cb3dddca97bec3d3681d0179f70c7367d Mon Oct 19 16:37:37 2020 -0700
    adding a quick IEDB wuhCor1 track docs page, #26305
  • lines changed 7, context: html, text, full: html, text
    e877f3bf71afc60465d83f5927c510b43aab2f48 Tue Oct 20 13:43:08 2020 -0700
    Minor changes to the validated epitopes desc page that was copied over from eboVir3 browser track refs #26305
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html
  • lines changed 4, context: html, text, full: html, text
    64700e05124913400006cfcaae0e94ac1331fe88 Tue Oct 20 12:18:18 2020 -0700
    Editing display notes, adding release date refs #26364
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 52, context: html, text, full: html, text
    d2b64fc2cb3878ce1c0a9b8512bc652e12994600 Mon Oct 19 10:13:58 2020 -0700
    Rename 'SARS-CoV-2 Phylo Pub' to 'Phylogeny: Public' and 'SARS-CoV-2 Phylogeny' to 'Phylogeny: GISAID' in order to make the difference between them more clear. Also hide the latter by default. refs #26364
  • lines changed 2, context: html, text, full: html, text
    5ccdd64cb512aba793f6a36676db6a69792bf923 Mon Oct 19 16:18:10 2020 -0700
    Removing 'tableBrowser off' setting from sarsCov2PhyloPub (copied by accident, thanks Daniel\!) refs #26364
  • lines changed 1, context: html, text, full: html, text
    64700e05124913400006cfcaae0e94ac1331fe88 Tue Oct 20 12:18:18 2020 -0700
    Editing display notes, adding release date refs #26364
  • lines changed 5, context: html, text, full: html, text
    f95eb610b88cbec2551e8fdde70923ed55fe591f Tue Oct 20 13:38:23 2020 -0700
    Releasing new validated epitopes track refs #26305
  • lines changed 51, context: html, text, full: html, text
    4bf9b63e4d757cda00e44bbc3b71c02bdbfa165e Wed Oct 21 14:21:03 2020 -0700
    Setting public phylo on by default refs #26364
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    7f2c8c7e74571f25d11da0dc618c95bc0bb5dd67 Wed Oct 21 13:03:00 2020 -0700
    Adding new utils phyloRenameAndPrune and vcfRenameAndPrune to top-level build target.
• src/hg/utils/phyloRenameAndPrune/makefile
  • lines changed 3, context: html, text, full: html, text
    edd8fa03488ce1ee3fa7b12b64de39ad0e3fc216 Wed Oct 21 12:57:36 2020 -0700
    New utils for making the public-sequences-only version of the SARS-CoV-2 Phylogeny track. Forgot to add these back in commit 0901c8be. refs #26364
• src/hg/utils/phyloRenameAndPrune/phyloRenameAndPrune.c
  • lines changed 84, context: html, text, full: html, text
    edd8fa03488ce1ee3fa7b12b64de39ad0e3fc216 Wed Oct 21 12:57:36 2020 -0700
    New utils for making the public-sequences-only version of the SARS-CoV-2 Phylogeny track. Forgot to add these back in commit 0901c8be. refs #26364
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 1, context: html, text, full: html, text
    66d46df506cdb2bcae62d8fbcfdfd4f97bc1a0c5 Tue Oct 20 11:59:10 2020 -0700
    Stop tdbQuery from complaining about valid filterValuesDefault trackDb setting
  • lines changed 1, context: html, text, full: html, text
    d807b60fd721c00051ac7e7cf5088eedba7170eb Thu Oct 22 13:28:01 2020 -0700
    in response to code review
• src/hg/utils/vcfRenameAndPrune/makefile
  • lines changed 3, context: html, text, full: html, text
    edd8fa03488ce1ee3fa7b12b64de39ad0e3fc216 Wed Oct 21 12:57:36 2020 -0700
    New utils for making the public-sequences-only version of the SARS-CoV-2 Phylogeny track. Forgot to add these back in commit 0901c8be. refs #26364
• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
  • lines changed 166, context: html, text, full: html, text
    edd8fa03488ce1ee3fa7b12b64de39ad0e3fc216 Wed Oct 21 12:57:36 2020 -0700
    New utils for making the public-sequences-only version of the SARS-CoV-2 Phylogeny track. Forgot to add these back in commit 0901c8be. refs #26364
• src/hg/utils/vcfToBed/vcfToBed.c
  • lines changed 2, context: html, text, full: html, text
    eb91bdbd593e04364d969b7461c1f690325da0e5 Tue Oct 20 16:39:13 2020 -0700
    Fix bug in ref/alt name shortening in vcfToBed, refs #25010
• src/inc/cheapcgi.h
  • lines changed 4, context: html, text, full: html, text
    feb380e4c526092d9793e1d70f8a484cca2ae338 Tue Oct 20 01:18:28 2020 -0700
    Fix speed of javascript in View, Facets, and Subtracks for hgTrackUi. fixes #26381
• src/inc/common.h
  • lines changed 7, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
• src/inc/htmlColor.h
  • lines changed 6, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    126705aca26f380da73ae4c8998bd64edd09118c Mon Oct 26 10:01:47 2020 -0700
    New version number v406
• src/inc/vcf.h
  • lines changed 1, context: html, text, full: html, text
    376a3438b1a96761c019bbe128908fc69b5083df Thu Jul 30 18:04:05 2020 -0700
    Adding VCF_NUM_COLS_BEFORE_GENOTYPES to vcf.h to reduce the proliferation of magic number 9's in the code.
• src/lib/cheapcgi.c
  • lines changed 12, context: html, text, full: html, text
    feb380e4c526092d9793e1d70f8a484cca2ae338 Tue Oct 20 01:18:28 2020 -0700
    Fix speed of javascript in View, Facets, and Subtracks for hgTrackUi. fixes #26381
• src/lib/common.c
  • lines changed 15, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
• src/lib/htmlColor.c
  • lines changed 19, context: html, text, full: html, text
    02f9444f186888d2da5d65d9db583ddf2d7b95ca Thu Oct 22 01:48:20 2020 -0700
    Adding trackDb options to change defaults for hic tracks. Also made some of those settings case-insensitive. refs #26312
• src/lib/linefile.c
  • lines changed 7, context: html, text, full: html, text
    358232fdd2fe9b78248b54fd38a9cd2f52ff4586 Wed Oct 21 12:49:05 2020 -0700
    lineFileUdcMayOpen automatically decompresses local files but not urls. netLineFileMayOpen does automatically decompress. For now, just use netLineFileMayOpen, although in the long term it would be better to ad support to lineFileUdcMayOpen to get the benefits of caching.
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    b00557148488a34f1d4ba7ed2a2b37264b33ea23 Tue Oct 20 13:02:44 2020 -0700
    Raise VCF_MAX_COLUMNS yet again -- sarscov2phylo latest release has >100,000 sequences\!
• src/utils/qa/weeklybld/buildEnv.csh
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    885995eafcdb9ae2d2f9c511ce6d36a1ab70ce0a Mon Oct 26 10:00:54 2020 -0700
    v406 final build

• lines changed: 1768
• files changed: 83