All File Changes

v378_base to v379_preview (2019-02-25 to 2019-03-04) v379

• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 11, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 6, context: html, text, full: html, text
    be389dc72daedc439d8a00cf2b09acfa8d41c38d Wed Feb 27 14:24:12 2019 -0800
    Yikes, hgIntegrator was not setting up udc! htslib was using its own network code.
  • lines changed 2, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
• src/hg/hgSession/backup.c
  • lines changed 1, context: html, text, full: html, text
    719a0f18aba33b58d3a3062c7f06ea65296586a6 Thu Feb 21 15:35:13 2019 -0800
    adding missing slash in end tag. This was not my doing. inherited code.
  • lines changed 21, context: html, text, full: html, text
    f154c7d4f9612d24dd047c593c949dd7b389b79e Wed Feb 27 12:29:58 2019 -0800
    code cleanup
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    719a0f18aba33b58d3a3062c7f06ea65296586a6 Thu Feb 21 15:35:13 2019 -0800
    adding missing slash in end tag. This was not my doing. inherited code.
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 61, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    40da01adf88860b52d384191692a0b0ce8662439 Wed Feb 27 16:41:55 2019 -0800
    oops... make sure table doesn't exist before assuming it doesn't exist #22885
• src/hg/hgTracks/extTools.c
  • lines changed 2, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    b8a81ed72bfd0502d0fd0cb4ed26517953ad032a Thu Feb 28 15:05:46 2019 -0800
    if being called through AJAX to draw a single track, make sure to load any composite parents as well. #23027
  • lines changed 73, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    b2ad359435d6780d389edcf3029cf70b67c5f27a Mon Feb 25 15:24:16 2019 -0800
    don't crash, but do abort, if a subtrack of a composite doesn't have a type #22541
  • lines changed 1, context: html, text, full: html, text
    8281d08d55c665e02c2b3daeed8efbdb144c05a0 Thu Feb 28 07:57:39 2019 -0800
    increase the size of a too small buffer
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 30, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgVai/libifyMe.c
  • lines changed 55, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgVai/libifyMe.h
  • lines changed 11, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    f56706efd48606f7211343afb57347aa0f116ec1 Tue Feb 26 13:25:06 2019 -0800
    Partly fixing bug in hgc where different results from the clicked item were displayed, refs #22996
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 8, context: html, text, full: html, text
    b971b945ce1f2015276965ed8b124634cee7bfa6 Wed Feb 27 06:04:03 2019 -0800
    fixing left margin problem for barchart plot, refs #21811
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 21, context: html, text, full: html, text
    191648a52ad534eb07be01e0ac15d33f118948e1 Fri Mar 1 16:00:48 2019 -0800
    Updating FAQ page _alt sequence + blog post ref#23040
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 59, context: html, text, full: html, text
    585ec51f88290d195b72e671bd30d55aace3bc70 Tue Feb 26 09:53:55 2019 -0800
    Reworded ncbiRefSeq section. Also updated TOC and uppercased GENCODE. refs #22970
  • lines changed 26, context: html, text, full: html, text
    da25a0a97925e3e95ad7cd7e3783ed6d3edf32c4 Fri Mar 1 16:02:13 2019 -0800
    More work on the unreleased genes FAQ page ref#22696
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 3, context: html, text, full: html, text
    f9c80af04a1b4e628890a6b23855b6635ee56e5b Fri Mar 1 14:16:30 2019 -0800
    Editing hgGeneGraph user guide for spelling/grammar, no refs#
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 14, context: html, text, full: html, text
    f634b3be908165b11d68ea44ab276a2187de71bd Wed Feb 27 15:48:43 2019 -0800
    Adding a section to the Session Help page about the short links to provide hints to mirrors and users. refs #23022
  • lines changed 27, context: html, text, full: html, text
    c4e3992db632194a308ab2405a53003fb641aa52 Fri Mar 1 11:19:10 2019 -0800
    Replacing code tags with button tags and correcting one button's wording
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 18, context: html, text, full: html, text
    b726c69421ca173060f54471548d92787d4e5964 Fri Mar 1 11:10:49 2019 -0800
    take out reference to stackoverflow and related code snippet #22783
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 11, context: html, text, full: html, text
    abb980117e48847d4b79d9f8235430076ec2bfda Mon Feb 25 12:56:37 2019 -0800
    Adding ncbi RefSeq HGMD release to newarch & indexNews, refs #22659
  • lines changed 4, context: html, text, full: html, text
    58ecb985ad0d2f5a69c0fba648a03142a8f85cf8 Tue Feb 26 13:29:29 2019 -0800
    editing announcement for HGMD track release, refs #22659
  • lines changed 0, context: html, text, full: html, text
    2306c71c6483dd17cbbb5f0a94d9b16f88ae2b1e Wed Feb 27 14:58:27 2019 -0800
    Adding edits for refSeq HGMD track release, refs #22659
  • lines changed 1, context: html, text, full: html, text
    0edeee5fbfb68a7dedd45e3e74f50bcf802c29b4 Wed Feb 27 15:10:51 2019 -0800
    More edits to refSeq HGMD, refs #22659
  • lines changed 2, context: html, text, full: html, text
    aaa96c576ebd2ab6cc8c5d605d5846a564746dad Fri Mar 1 14:48:29 2019 -0800
    Editing an old news post title so that the HTML code is less than 100 characters per line, no Redmine.
• src/hg/htdocs/indexNews.html
  • lines changed 2, context: html, text, full: html, text
    abb980117e48847d4b79d9f8235430076ec2bfda Mon Feb 25 12:56:37 2019 -0800
    Adding ncbi RefSeq HGMD release to newarch & indexNews, refs #22659
  • lines changed 1, context: html, text, full: html, text
    2306c71c6483dd17cbbb5f0a94d9b16f88ae2b1e Wed Feb 27 14:58:27 2019 -0800
    Adding edits for refSeq HGMD track release, refs #22659
• src/hg/hubApi/apiUtils.c
  • lines changed 16, context: html, text, full: html, text
    d5cbd45d0d3db423db2dbad15c653961c0bd29ac Wed Feb 27 13:57:14 2019 -0800
    one stop shopping for trackDb now in obtainTdb() function refs #18869
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    d5cbd45d0d3db423db2dbad15c653961c0bd29ac Wed Feb 27 13:57:14 2019 -0800
    one stop shopping for trackDb now in obtainTdb() function refs #18869
• src/hg/hubApi/getData.c
  • lines changed 1, context: html, text, full: html, text
    d5cbd45d0d3db423db2dbad15c653961c0bd29ac Wed Feb 27 13:57:14 2019 -0800
    one stop shopping for trackDb now in obtainTdb() function refs #18869
  • lines changed 90, context: html, text, full: html, text
    6ec964d05444b3c2f8147cd678de79ec5254b97a Wed Feb 27 15:49:57 2019 -0800
    output data from bigBed and bigWig track types for native database track refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 207, context: html, text, full: html, text
    b6ea7e02e7c946b1cb700d3cab07decce272d4c7 Tue Feb 26 16:00:40 2019 -0800
    better counting of legitimate tracks refs #18869
  • lines changed 7, context: html, text, full: html, text
    a623f8b7d5f5d7ad88a33e7a0cba4a91f76800ac Tue Feb 26 17:53:14 2019 -0800
    catch up list functions to recent revisions to getting trackDb refs #18869
  • lines changed 4, context: html, text, full: html, text
    d5cbd45d0d3db423db2dbad15c653961c0bd29ac Wed Feb 27 13:57:14 2019 -0800
    one stop shopping for trackDb now in obtainTdb() function refs #18869
  • lines changed 10, context: html, text, full: html, text
    6ec964d05444b3c2f8147cd678de79ec5254b97a Wed Feb 27 15:49:57 2019 -0800
    output data from bigBed and bigWig track types for native database track refs #18869
• src/hg/hubApi/list.c
  • lines changed 6, context: html, text, full: html, text
    a623f8b7d5f5d7ad88a33e7a0cba4a91f76800ac Tue Feb 26 17:53:14 2019 -0800
    catch up list functions to recent revisions to getting trackDb refs #18869
  • lines changed 18, context: html, text, full: html, text
    d5cbd45d0d3db423db2dbad15c653961c0bd29ac Wed Feb 27 13:57:14 2019 -0800
    one stop shopping for trackDb now in obtainTdb() function refs #18869
  • lines changed 9, context: html, text, full: html, text
    6ec964d05444b3c2f8147cd678de79ec5254b97a Wed Feb 27 15:49:57 2019 -0800
    output data from bigBed and bigWig track types for native database track refs #18869
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 4, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/inc/hgFind.h
  • lines changed 17, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/js/jquery.plugins.js
  • lines changed 70, context: html, text, full: html, text
    818e5c3483440c33fba69b82fb8801ce797ecf00 Fri Mar 1 15:01:59 2019 -0800
    take out some code from stackoverlow and the code that required it. Add copyright message to hoverIntent code. #22783
• src/hg/lib/cart.c
  • lines changed 4, context: html, text, full: html, text
    8a12d4808bd304a353c77bf2eed9ade16578172a Tue Feb 26 14:18:44 2019 -0800
    when we're disconnecting assembly hubs, we need to remove any custom tracks loaded on it
  • lines changed 19, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 30, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
  • lines changed 4, context: html, text, full: html, text
    0283f0d3e96fe85f11241197f477611680c01186 Mon Mar 4 09:58:59 2019 -0800
    cartWebStart adds a hidden <input> to set db on every page. However, some CGIs pass in NULL for db, so db is set to '(null)'. Don't make the <input> unless a value is passed in.
• src/hg/lib/hgFind.c
  • lines changed 233, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    3f661bcfef779274a734a4d31637c0df55a48102 Wed Feb 27 16:28:06 2019 -0800
    Only hgVai uses webStart() and does not need the old logo .jpg, so call webStartWrapper withLogo=FALSE. sorta refs #22945
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/cooccurrenceCounts.c
  • lines changed 710, context: html, text, full: html, text
    8b6dbf2a8c454f92a7e18bc6c7f200f02833fbc8 Thu Feb 28 16:48:47 2019 -0800
    Error log crawler that makes a coocurrence matrix of tracks used together, refs #21785
  • lines changed 119, context: html, text, full: html, text
    5b714783c16411b99dbd130b36ae39a7208e9b8d Mon Mar 4 10:10:29 2019 -0800
    Fixing some small bugs and adding some error checking to track matrix crawler
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/makefile
  • lines changed 3, context: html, text, full: html, text
    8b6dbf2a8c454f92a7e18bc6c7f200f02833fbc8 Thu Feb 28 16:48:47 2019 -0800
    Error log crawler that makes a coocurrence matrix of tracks used together, refs #21785
• src/hg/makeDb/doc/GRCm38B/initialBuild.txt
  • lines changed 993, context: html, text, full: html, text
    d87cca9bea19e4c0ff054dacf01037d76f46730a Thu Feb 28 15:50:09 2019 -0800
    initial build rmsk underway refs #22271
• src/hg/makeDb/doc/GRCm38B/transName.pl
  • lines changed 52, context: html, text, full: html, text
    d87cca9bea19e4c0ff054dacf01037d76f46730a Thu Feb 28 15:50:09 2019 -0800
    initial build rmsk underway refs #22271
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    e9be36c735264edba20ec1a96bd4eea07ca0c00c Tue Feb 26 08:18:15 2019 -0800
    adding mastermind make docs and scripts, refs #21895
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 20, context: html, text, full: html, text
    4339c1c9b6e426b0d215f404638f775c78b25f99 Fri Mar 1 11:30:46 2019 -0800
    Added GRCm38B; refs #22271
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    f2bcdfe93aa1f29a64c5d90d879b26cb61459e0e Fri Mar 1 11:32:15 2019 -0800
    Added GRCm38B - mouse refs #22271
• src/hg/makeDb/genbank/src/download/gbDownloadStep
  • lines changed 7, context: html, text, full: html, text
    3ac2921a9eb176140ba92926412313339844a7d2 Mon Feb 25 12:20:00 2019 -0800
    require manual intervention when the genbank release changes because they're leaving the dailies in place for some number of days after the release is incremented.
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    e047c335a4eca0ce8efab277bc16007acafb79e4 Mon Feb 25 12:27:35 2019 -0800
    oops... try this again.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    d092319f15d3ef1b82c81b3c24ecfcecfdcca492 Fri Mar 1 13:28:02 2019 -0800
    Adding GRCm pointing to mmNames refs #22271
• src/hg/makeDb/mastermind/mastermind.as
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    e9be36c735264edba20ec1a96bd4eea07ca0c00c Tue Feb 26 08:18:15 2019 -0800
    adding mastermind make docs and scripts, refs #21895
• src/hg/makeDb/mastermind/mastermindToBed.py
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    e9be36c735264edba20ec1a96bd4eea07ca0c00c Tue Feb 26 08:18:15 2019 -0800
    adding mastermind make docs and scripts, refs #21895
• src/hg/makeDb/trackDb/crispr.html
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    02cfe5b9327285bfb94e01f14d470a7ac949e8c0 Tue Feb 26 08:13:27 2019 -0800
    adding Hiram to crispr tracks page, no redmine
• src/hg/makeDb/trackDb/crispr10K.html
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    80a5b5305484b869968b21f6344c2fb2c3034af3 Tue Feb 26 05:34:56 2019 -0800
    adding note about scoring change to crispr 10k track, no redmine, email from Tanya Granchrova at Allan Brain Atlas
• src/hg/makeDb/trackDb/human/hg19/mastermind.html
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    a4692dfa67a1708289b2866a2bfc732d6910d209 Fri Mar 1 14:14:06 2019 -0800
    Editing mastermind track description page, refs #21895
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    a4692dfa67a1708289b2866a2bfc732d6910d209 Fri Mar 1 14:14:06 2019 -0800
    Editing mastermind track description page, refs #21895
• src/hg/makeDb/trackDb/makefile
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    e9a106cdaa233883c628a223ab3265c85427b0b9 Thu Feb 28 14:31:09 2019 -0800
    initial files for GRCm38B refs #22271
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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    8973d8ba552779243daa2b127a8c3bca971b9d81 Fri Mar 1 08:46:25 2019 -0800
    Updating http to https for calJac3, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/GRCm38B/description.html
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    e9a106cdaa233883c628a223ab3265c85427b0b9 Thu Feb 28 14:31:09 2019 -0800
    initial files for GRCm38B refs #22271
• src/hg/makeDb/trackDb/mouse/GRCm38B/gap.html
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    e9a106cdaa233883c628a223ab3265c85427b0b9 Thu Feb 28 14:31:09 2019 -0800
    initial files for GRCm38B refs #22271
• src/hg/makeDb/trackDb/mouse/GRCm38B/gold.html
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    e9a106cdaa233883c628a223ab3265c85427b0b9 Thu Feb 28 14:31:09 2019 -0800
    initial files for GRCm38B refs #22271
• src/hg/makeDb/trackDb/mouse/GRCm38B/trackDb.ra
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    e9a106cdaa233883c628a223ab3265c85427b0b9 Thu Feb 28 14:31:09 2019 -0800
    initial files for GRCm38B refs #22271
• src/hg/makeDb/trackDb/mouse/mm10/singleCell.html
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    00fecf2589600ae0fc736840b84f6fd61f5308cd Thu Feb 28 11:56:32 2019 -0800
    Adding more information about the barChart height visible on hgTracks and the boxplot. refs #21811
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    5603035542d04a36bf99b0aae57397ecf41f75ca Fri Mar 1 10:13:08 2019 -0800
    Changing the track name from 'singleCell' to 'tabulaMuris'. Also renaming the Tabula Muris description page from 'singleCell.html' to 'tabulaMuris.html', refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/tabulaMuris.html
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    5603035542d04a36bf99b0aae57397ecf41f75ca Fri Mar 1 10:13:08 2019 -0800
    Changing the track name from 'singleCell' to 'tabulaMuris'. Also renaming the Tabula Muris description page from 'singleCell.html' to 'tabulaMuris.html', refs #21811
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    3524c37285ae95d2378f4e9dd71202cbbad1eca2 Fri Mar 1 16:19:15 2019 -0800
    Changing 'single RNA-seq cell' to 'single cell RNA-seq', refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
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    ee77efd370267585db4d4b719e87ff331efabc76 Wed Feb 27 06:33:49 2019 -0800
    rearranging tabula muris tracks as per Jim, refs #21811
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    5115346eab4f7f9c6727c899266d92b69f89f379 Wed Feb 27 06:41:45 2019 -0800
    more tweaks to tabula muris, refs #21811
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    cfbd71934043451eb3d1d9d62fcaf149695b7fb3 Wed Feb 27 14:12:28 2019 -0800
    Adding the singleCell.html page to the new composite tracks now that there are no views, refs #21811
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    fd0b91f16f2312bc603ac654bc8efb465f3b0eab Wed Feb 27 15:13:46 2019 -0800
    Adding a missing 's' to Muris, refs #21811
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    95c1d1c5c95ec47e4462873d7a7cc354752b0fc4 Thu Feb 28 14:40:40 2019 -0800
    Changing the shortLabel to 'Tabula Muris' as per Jim's request, refs #21811
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    5603035542d04a36bf99b0aae57397ecf41f75ca Fri Mar 1 10:13:08 2019 -0800
    Changing the track name from 'singleCell' to 'tabulaMuris'. Also renaming the Tabula Muris description page from 'singleCell.html' to 'tabulaMuris.html', refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    00aa663fe31530e5679b75c422e6e078cbdb845a Thu Feb 28 15:20:37 2019 -0800
    Adding the beta release tag for the tabula muris track, refs #21811
• src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.html
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    c56454b8b92edafb00ade2538f01e0e88282fba0 Mon Mar 4 08:40:55 2019 -0800
    Updating redirected links for ce11, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
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    c56454b8b92edafb00ade2538f01e0e88282fba0 Mon Mar 4 08:40:55 2019 -0800
    Updating redirected links for ce11, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
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    c56454b8b92edafb00ade2538f01e0e88282fba0 Mon Mar 4 08:40:55 2019 -0800
    Updating redirected links for ce11, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/chainSelf.html
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    c56454b8b92edafb00ade2538f01e0e88282fba0 Mon Mar 4 08:40:55 2019 -0800
    Updating redirected links for ce11, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ws245Genes.html
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    c56454b8b92edafb00ade2538f01e0e88282fba0 Mon Mar 4 08:40:55 2019 -0800
    Updating redirected links for ce11, uiLinks cronjob.
• src/hg/pyLib/hgLib.py
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    34b790e2381539fa6830bd2129c5089f44be4595 Tue Feb 26 02:14:18 2019 -0800
    making hgGeneGraph bottleneck penalty stricter, refs #22999
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    e13edc60a0c6486b8b4ad715e12683b28f6eb166 Tue Feb 26 02:59:37 2019 -0800
    fix debug messages and bot delay system in hgGeneGraph, refs #22999
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    ab24e76f229a7159903ed55f6374127f29ffe446 Tue Feb 26 03:11:16 2019 -0800
    adding constants and one more fix to botdelay system in gene graph, refs #22999
• src/hg/utils/makefile
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    3bf826d56ae3bc51514dbd0dbf8e7e96328fb4cb Mon Feb 25 13:00:42 2019 -0800
    Adding hubClone util to userApps, refs #13428
• src/hg/utils/twoBitMask/twoBitMask.c
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    8c4dcf0266b308deb36190efb151308cbc4d267e Mon Feb 25 13:28:09 2019 -0800
    fix bug in twoBitMask where it was using a value that had already been freed #22704
• src/lib/annoStreamVcf.c
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    49a9e46f48bc7872a655527694e027e51aa46f38 Wed Feb 27 12:19:38 2019 -0800
    Oops, forgot to check for NULL in a corner case: VCF file has records only in chromosomes preceding the query region chrom.
• src/lib/cheapcgi.c
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    6ad610566091450adc69bf9f321ac57f38a3d9d2 Wed Feb 27 12:18:03 2019 -0800
    Add more info to 'Short POST input' error message.
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    0714ad987fb4018da001e4ec75a9288207f902cf Fri Mar 1 14:14:45 2019 -0800
    Revert "When hgTables gets multiple search results, hgFind calls webEnd and then hgTables needs to do cartWebEnd, so jsInlineFinish is called twice. Until the webStart/webEnd can be factored out of hgFind.c, prevent the jsInlineFinish warning from bothering the user. refs #22945" webStart/webEnd has been factored out of hgFind, so hgTables can open and close the page cleanly and there's no warning to hide from the user. This reverts commit ee3659b05d0af22a52207792b8deaf836a727fe5.
• src/utils/git-reports/git-reports.c
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    992790314a60edd73f82882faf6b438e005fdcc0 Mon Feb 25 19:13:36 2019 -0800
    Fixing weird rare case with no files listed. Sort of an empty commit with same tree but a new commit and message.
• src/utils/makefile
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    98d723e403eff543a9075b4982272907c5c58120 Wed Feb 27 06:14:23 2019 -0800
    adding trackDbRename tool, created to rename tabula muris tracks
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    9e42bf8546abb0abc46036b726c8a25515db80a0 Thu Feb 28 05:08:28 2019 -0800
    adding tool for sorting of a trackDb (e.g. trackHub) file. no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    08214e2c6f4dfd39a2631694123c2976eba367f4 Mon Mar 4 10:17:29 2019 -0800
    v379 preview1, refs #22942
• src/utils/tdbRename
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    9e42bf8546abb0abc46036b726c8a25515db80a0 Thu Feb 28 05:08:28 2019 -0800
    adding tool for sorting of a trackDb (e.g. trackHub) file. no redmine
• src/utils/tdbSort
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    9e42bf8546abb0abc46036b726c8a25515db80a0 Thu Feb 28 05:08:28 2019 -0800
    adding tool for sorting of a trackDb (e.g. trackHub) file. no redmine
• src/utils/trackDbRename
  • lines changed 92, context: html, text, full: html, text
    98d723e403eff543a9075b4982272907c5c58120 Wed Feb 27 06:14:23 2019 -0800
    adding trackDbRename tool, created to rename tabula muris tracks
  • lines changed 92, context: html, text, full: html, text
    9e42bf8546abb0abc46036b726c8a25515db80a0 Thu Feb 28 05:08:28 2019 -0800
    adding tool for sorting of a trackDb (e.g. trackHub) file. no redmine

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