All File Changes

v377_preview to v377_preview2 (2019-01-21 to 2019-01-28) v377

• confs/asia.hg.conf
  • lines changed 122, context: html, text, full: html, text
    55e011984f93b9a7310176e5d29e8c45597e20e0 Wed Jan 23 14:35:50 2019 -0800
    Adding automatically-updated copies of the hg.conf files from our European and Asian mirror servers, no ticket
  • lines changed 3, context: html, text, full: html, text
    a0f08908b43bb766a8d71873dd7e0823574642a8 Sun Jan 27 01:11:49 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 120, context: html, text, full: html, text
    55e011984f93b9a7310176e5d29e8c45597e20e0 Wed Jan 23 14:35:50 2019 -0800
    Adding automatically-updated copies of the hg.conf files from our European and Asian mirror servers, no ticket
  • lines changed 3, context: html, text, full: html, text
    a0f08908b43bb766a8d71873dd7e0823574642a8 Sun Jan 27 01:11:49 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/preview.hg.conf
  • lines changed 1, context: html, text, full: html, text
    a0f08908b43bb766a8d71873dd7e0823574642a8 Sun Jan 27 01:11:49 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    a0f08908b43bb766a8d71873dd7e0823574642a8 Sun Jan 27 01:11:49 2019 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 2, context: html, text, full: html, text
    0f5af7af5f4c328a8f9aba5384443593db8917a9 Thu Jan 24 13:28:25 2019 -0800
    Changing Best Practices to Standards in menu bar.
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 2, context: html, text, full: html, text
    0f5af7af5f4c328a8f9aba5384443593db8917a9 Thu Jan 24 13:28:25 2019 -0800
    Changing Best Practices to Standards in menu bar.
• src/hg/hgTracks/hgTracks.c
  • lines changed 112, context: html, text, full: html, text
    f621f87f73fd614e27adc747ba3ff044d2b4c4ad Sat Jan 26 08:15:56 2019 -0800
    Be smarter about setting track visibilities on the URL, including dealing with super tracks, composites, and setting hub visibilities without hub_ decoration. Also, add ignoreCookies URL variable so folks can link to a default cart. #18544
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    c59971839b9baa4b99e670239fab8650517b10b9 Fri Jan 25 09:17:17 2019 -0800
    I think we can expose the command that failed, for mirrors this helps a bit, refs #22833
  • lines changed 7, context: html, text, full: html, text
    399d53a062f79a497d2f8dcbb3e3af5dea30cd0a Mon Jan 28 02:36:17 2019 -0800
    adding a oldFonts option to barchart hgc page for QA, refs #21881
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 69, context: html, text, full: html, text
    7c689c0a5884284c60ac21251023fdc2d83f4ef7 Thu Jan 24 07:12:50 2019 -0800
    trying to make the barchart boxplot a bit nicer, especially for many labels, refs #22838
  • lines changed 15, context: html, text, full: html, text
    c75c01edb41bd0ba9f85bb3e4137d5643bf94d86 Fri Jan 25 09:15:12 2019 -0800
    do not require or try to install the showtext R package anymore, refs #22833
  • lines changed 11, context: html, text, full: html, text
    399d53a062f79a497d2f8dcbb3e3af5dea30cd0a Mon Jan 28 02:36:17 2019 -0800
    adding a oldFonts option to barchart hgc page for QA, refs #21881
  • lines changed 1, context: html, text, full: html, text
    2437f9b3087d90b80ffa429ec7642e7cb46e071b Mon Jan 28 03:06:04 2019 -0800
    increase margin for y-axis label in barchart graph, refs #21881
  • lines changed 5, context: html, text, full: html, text
    56aebf53596239034b6e26d0b761b7e66dbf7bda Mon Jan 28 03:28:51 2019 -0800
    not changing normal gtex plot direction anymore, refs #22838
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    1fcc392fed48b0f7fd95f068cd51ca5a21cb37b5 Fri Jan 25 09:18:27 2019 -0800
    Fixing double quotes on _blank anchors ref#22820
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 8, context: html, text, full: html, text
    a42abd0fafd3d2bf6e4659a85c8ff58d5bfe3a0e Wed Jan 23 09:42:51 2019 -0800
    Fixing >100 char line for code review #22821
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 1, context: html, text, full: html, text
    64dfe04e8d4cff269a030c914de6f3f11f76bf62 Thu Jan 24 11:14:52 2019 -0800
    Stumbled on this error, example 11 should be example 5
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 7, context: html, text, full: html, text
    8a13fe93103a4914aa414b1780f04dc3ae103d49 Thu Jan 24 16:56:07 2019 -0800
    Adding relevant embedded video to help pages #22486
  • lines changed 2, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 5, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 12, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 24, context: html, text, full: html, text
    8a13fe93103a4914aa414b1780f04dc3ae103d49 Thu Jan 24 16:56:07 2019 -0800
    Adding relevant embedded video to help pages #22486
  • lines changed 19, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 7, context: html, text, full: html, text
    8a13fe93103a4914aa414b1780f04dc3ae103d49 Thu Jan 24 16:56:07 2019 -0800
    Adding relevant embedded video to help pages #22486
  • lines changed 4, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 3, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    c5ec515a886286ad4fbb96d64a910ce0398fe57b Wed Jan 23 17:16:25 2019 -0800
    Adding three conservation tracks to newsArch
  • lines changed 1, context: html, text, full: html, text
    72510199a63fe02f423395bde6a52d261cb0bdda Wed Jan 23 17:27:52 2019 -0800
    Updating news entries to include recent tranck release #22687
  • lines changed 24, context: html, text, full: html, text
    69ede9d145d0a35b7c64dc57c80ab1cd2aec00a9 Thu Jan 24 12:19:09 2019 -0800
    Added date, added another bootstrap column for 3 cons track release #22687
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 4, context: html, text, full: html, text
    8a13fe93103a4914aa414b1780f04dc3ae103d49 Thu Jan 24 16:56:07 2019 -0800
    Adding relevant embedded video to help pages #22486
  • lines changed 1, context: html, text, full: html, text
    1286b6ef6124539b80fadf97dc6bfb54a9cb6634 Fri Jan 25 14:41:06 2019 -0800
    Adding videos to help docs and/or removing suggested videos popups #22486
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    72510199a63fe02f423395bde6a52d261cb0bdda Wed Jan 23 17:27:52 2019 -0800
    Updating news entries to include recent tranck release #22687
• src/hg/hubApi/hubApi.c
  • lines changed 173, context: html, text, full: html, text
    800586745616553f76c9c435f0a4fb89db39c976 Thu Jan 24 11:07:58 2019 -0800
    checking bbi file stats needs errCatch refs #18869
  • lines changed 166, context: html, text, full: html, text
    73c3b813ef766a41c1e44e4f2e17c4757ac155eb Fri Jan 25 09:51:26 2019 -0800
    public hubs on drop down menu and other hub entry box plus time out to exit on long running queries refs #18869
  • lines changed 113, context: html, text, full: html, text
    8271809bdf0f5052d48956d65e77e43fb0ea84ad Fri Jan 25 14:05:53 2019 -0800
    now recognizing all known hub track types refs #18869
  • lines changed 281, context: html, text, full: html, text
    813ac14a66f960ceb9a2c8e56054664181c8d35b Sun Jan 27 21:20:09 2019 -0800
    output valid json for public hub listing refs #18869
• src/hg/hubApi/makefile
  • lines changed 1, context: html, text, full: html, text
    813ac14a66f960ceb9a2c8e56054664181c8d35b Sun Jan 27 21:20:09 2019 -0800
    output valid json for public hub listing refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 89, context: html, text, full: html, text
    3fd5e288f2944afa0ee8f9bf72ccbc67b63ab4c0 Mon Jan 28 10:13:04 2019 -0800
    beginning of a consumer procedure refs #18869
• src/hg/lib/cart.c
  • lines changed 4, context: html, text, full: html, text
    f621f87f73fd614e27adc747ba3ff044d2b4c4ad Sat Jan 26 08:15:56 2019 -0800
    Be smarter about setting track visibilities on the URL, including dealing with super tracks, composites, and setting hub visibilities without hub_ decoration. Also, add ignoreCookies URL variable so folks can link to a default cart. #18544
• src/hg/lib/wikiLink.c
  • lines changed 2, context: html, text, full: html, text
    6b0f0759060bdea5837b13dea9dc58ee6654f3de Thu Jan 24 12:28:43 2019 -0800
    Changing login.acceptIdx default to false, as I should have done 2 years ago. refs #17327
• src/hg/makeDb/doc/hg38/ncbiRefSeqGenomicDiff.txt
  • lines changed 4, context: html, text, full: html, text
    9d7ae21a4ce62a41658af847358a60be3bb6f742 Fri Jan 25 12:55:33 2019 -0800
    Adding patch sequence annotations to hg38 ncbiRefSeqGenomicDiff. refs #18853, #18855 notes 51, 53
• src/hg/makeDb/doc/hg38/patchUpdate.11.txt
  • lines changed 106, context: html, text, full: html, text
    f4dbc5c6e419491e0891ae0ee0a1b01261fbe6fb Wed Jan 23 17:49:25 2019 -0800
    Added GRCh38.p11 and p12 sequences to ENCODE Regulation tracks that are not visible by default (DNase HS, DNase Signal). refs #18855, #18853
• src/hg/makeDb/doc/hg38/patchUpdate.12.txt
  • lines changed 93, context: html, text, full: html, text
    f4dbc5c6e419491e0891ae0ee0a1b01261fbe6fb Wed Jan 23 17:49:25 2019 -0800
    Added GRCh38.p11 and p12 sequences to ENCODE Regulation tracks that are not visible by default (DNase HS, DNase Signal). refs #18855, #18853
  • lines changed 24, context: html, text, full: html, text
    9d7ae21a4ce62a41658af847358a60be3bb6f742 Fri Jan 25 12:55:33 2019 -0800
    Adding patch sequence annotations to hg38 ncbiRefSeqGenomicDiff. refs #18853, #18855 notes 51, 53
• src/hg/makeDb/genbank/etc/validateDb.sh
  • lines changed 13, context: html, text, full: html, text
    c7dcf1601be1eb1cf9ef629a874f75587cd2eccd Tue Jan 22 11:39:42 2019 -0800
    delete some commented out lines per code review #22826
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 10, context: html, text, full: html, text
    60f05972f2081e53059426fffe39397021e32aa4 Wed Jan 23 10:30:38 2019 -0800
    Add fix sequences to hg38/hg19 gateway pages ref#22806
  • lines changed 1, context: html, text, full: html, text
    0aa1fca1fb58fa75f04e15c80d84521ff3062f2c Wed Jan 23 13:50:15 2019 -0800
    Fixing a sentence hg19 gateway ref#22806
• src/hg/makeDb/trackDb/human/hg19/mastermind.html
  • lines changed 86, context: html, text, full: html, text
    29d8327a4526bdfc77ea6ffc1e1d02111562f040 Mon Jan 28 03:47:44 2019 -0800
    adding mastermind docs page, refs #21895
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 44, context: html, text, full: html, text
    60f05972f2081e53059426fffe39397021e32aa4 Wed Jan 23 10:30:38 2019 -0800
    Add fix sequences to hg38/hg19 gateway pages ref#22806
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 1, context: html, text, full: html, text
    1a157b44250a441d1ccb6b94a01a896e56ff8de2 Tue Jan 22 01:45:45 2019 -0800
    fixing genehancer outlinks, refs #22184
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
  • lines changed 149, context: html, text, full: html, text
    1fcc392fed48b0f7fd95f068cd51ca5a21cb37b5 Fri Jan 25 09:18:27 2019 -0800
    Fixing double quotes on _blank anchors ref#22820
• src/hg/utils/hubClone/hubClone.c
  • lines changed 273, context: html, text, full: html, text
    2cada58a134c19e03703162be7ab8673d9ddf381 Thu Jan 24 15:30:28 2019 -0800
    New hubClone utility for copying a remote hub to local and changing bigDataUrls to remote
• src/hg/utils/hubClone/makefile
  • lines changed 3, context: html, text, full: html, text
    2cada58a134c19e03703162be7ab8673d9ddf381 Thu Jan 24 15:30:28 2019 -0800
    New hubClone utility for copying a remote hub to local and changing bigDataUrls to remote
• src/lib/vcf.c
  • lines changed 2, context: html, text, full: html, text
    7413e7df50cd60ee13b79af99c6acbbe09215530 Fri Jan 25 12:42:25 2019 -0800
    Accept VCF v4.3. We don't implement the full spec, but 1000 Genomes just released very simple VCF for GRCh38 that says it's v4.3 and we have to support them.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    12db679542a539dfafaee07be5a0fde842c7b174 Mon Jan 28 10:11:41 2019 -0800
    v377 preview2, refs #TICKETID

• lines changed: 2272
• files changed: 57