All File Changes

v382_base to v383_preview (2019-05-20 to 2019-05-27) v383

• confs/asia.hg.conf
  • lines changed 127, context: html, text, full: html, text
    d5d03d5ddbe1c3b2ad92d8c93ef5104a4787f249 Sun May 26 01:11:42 2019 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    ed5a26645b585f95f391c8bc3b37c2d125d12a90 Wed May 22 12:06:19 2019 -0700
    Commenting out shortLink line that makes hgSession links unusable #22440
  • lines changed 1, context: html, text, full: html, text
    d5d03d5ddbe1c3b2ad92d8c93ef5104a4787f249 Sun May 26 01:11:42 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgSession/convertUserSessions.sh
  • lines changed 55, context: html, text, full: html, text
    61bd70ac016c2b0691753bb0f5acafc7bf2ad53b Tue May 14 09:49:16 2019 -0700
    Adding convertUserSessions.sh and sessionDataConvert.sh for bulk conversion of old saved sessions to use sessionDataDir/sessionDataDbPrefix. refs #22440
  • lines changed 1, context: html, text, full: html, text
    85188ac087873b2964fcfbc3426694ca68bdd489 Wed May 22 10:33:21 2019 -0700
    Reducing delay between calls to sessionDataConvert.sh because it's fairly lightweight and there are a lot of sessions to convert. refs #22440
• src/hg/hgSession/hgSession.c
  • lines changed 87, context: html, text, full: html, text
    fd526976ba5971d4bae14235cf2f735751a5e548 Wed May 15 14:26:41 2019 -0700
    Adding doReSaveSession to streamline loading and saving a session in one CGI request, for converting old session trash paths and customTrash tables to userdata and customData. refs #22440
  • lines changed 26, context: html, text, full: html, text
    4c63c358efeed6aaf99fad3993e63123cd6a0f79 Wed May 22 10:30:58 2019 -0700
    Use errCatch to avoid errAborts when re-saving sessions whose db has been removed. refs #22440
  • lines changed 7, context: html, text, full: html, text
    45764c815bb96401f97540ca20ef0b09f67cdcf2 Fri May 24 13:37:21 2019 -0700
    When re-saving session, preserve shared column which is not a boolean but rather {0, 1, 2=public session}. refs #22440 note-170
• src/hg/hgSession/hgSession.h
  • lines changed 5, context: html, text, full: html, text
    fd526976ba5971d4bae14235cf2f735751a5e548 Wed May 15 14:26:41 2019 -0700
    Adding doReSaveSession to streamline loading and saving a session in one CGI request, for converting old session trash paths and customTrash tables to userdata and customData. refs #22440
• src/hg/hgSession/sessionData.c
  • lines changed 4, context: html, text, full: html, text
    13e46137c78bb4ba2e27e913c958715c0508fdd6 Tue May 21 12:39:53 2019 -0700
    Fix missing hFreeConn that caused 'too many open connections' error for sessions with lots of dbTable custom tracks. refs #22440
  • lines changed 3, context: html, text, full: html, text
    8a0285e2e86e8d604b21e1cc2a5cfaef4c28c00e Wed May 22 11:29:22 2019 -0700
    Look out for loss of files in cart var ss, in addition to hgPcrResult_*. refs #22440
• src/hg/hgSession/sessionDataConvert.sh
  • lines changed 93, context: html, text, full: html, text
    61bd70ac016c2b0691753bb0f5acafc7bf2ad53b Tue May 14 09:49:16 2019 -0700
    Adding convertUserSessions.sh and sessionDataConvert.sh for bulk conversion of old saved sessions to use sessionDataDir/sessionDataDbPrefix. refs #22440
  • lines changed 1, context: html, text, full: html, text
    e64d62b5403c486838f43bf4d1283c3230840fea Wed May 22 10:31:45 2019 -0700
    Adding quotes necessary for dealing with decoded usernames that end with space(s). refs #22440
• src/hg/hgTracks/lollyTrack.c
  • lines changed 5, context: html, text, full: html, text
    82f9f3d9964a3965647fff81381d2bec0ac29b79 Mon May 20 14:36:17 2019 -0700
    oops, need to clone some memory passed into lollyMethods
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 21, context: html, text, full: html, text
    87eae20de868054a5abeedeb78a24d3e296b87d5 Tue May 21 15:09:55 2019 -0700
    Adding notes about TinyURL enabling URL parameters #23030
  • lines changed 10, context: html, text, full: html, text
    220420c493c9dd3d509cd6fb6084b3bf756d8ef4 Fri May 24 12:09:02 2019 -0700
    Making b0b's CR changes #23528
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    07c3eb3c86e6a0888f94782ca4ccaff69d14ea7f Tue May 21 15:39:34 2019 -0700
    Adding comma to date of 3 assembly releases & changing felCat9 release date on credits.html, refs #23527
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 3, context: html, text, full: html, text
    6e67ef8295bba3ef3ab3cb5fcff3761328c47109 Tue May 21 15:56:30 2019 -0700
    Making small changes in response to CR
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    87eae20de868054a5abeedeb78a24d3e296b87d5 Tue May 21 15:09:55 2019 -0700
    Adding notes about TinyURL enabling URL parameters #23030
  • lines changed 72, context: html, text, full: html, text
    220420c493c9dd3d509cd6fb6084b3bf756d8ef4 Fri May 24 12:09:02 2019 -0700
    Making b0b's CR changes #23528
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 6, context: html, text, full: html, text
    87eae20de868054a5abeedeb78a24d3e296b87d5 Tue May 21 15:09:55 2019 -0700
    Adding notes about TinyURL enabling URL parameters #23030
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 3, context: html, text, full: html, text
    1bdcc1481904105feca1fd7f6069bf693fbb2246 Fri May 24 10:54:06 2019 -0700
    Adding fixes suggested by bob in the code review, #23489
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 6, context: html, text, full: html, text
    7256fc988f7c507cb182f73ad49efc4baf383778 Wed May 22 09:48:18 2019 -0700
    Forgot to commit my changes to mirrorManual.html from last week's code review, CR #23491
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    918a8278d02c4e8d7e79c693ad1f1263abeedee3 Tue May 21 08:51:57 2019 -0700
    adding cat to indexNews and newsarch.html for felCat9 release, refs #21043
  • lines changed 3, context: html, text, full: html, text
    07c3eb3c86e6a0888f94782ca4ccaff69d14ea7f Tue May 21 15:39:34 2019 -0700
    Adding comma to date of 3 assembly releases & changing felCat9 release date on credits.html, refs #23527
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    918a8278d02c4e8d7e79c693ad1f1263abeedee3 Tue May 21 08:51:57 2019 -0700
    adding cat to indexNews and newsarch.html for felCat9 release, refs #21043
• src/hg/htdocs/training/index.html
  • lines changed 2, context: html, text, full: html, text
    06b29abfe16d259fcfd9403acc2dbf35eb54e3f9 Wed May 22 11:34:20 2019 -0700
    Some minor errors by hubCheck, no RM
  • lines changed 5, context: html, text, full: html, text
    7593be5d1ee71d0d7e827f6d423cbec2a4a35126 Wed May 22 12:36:23 2019 -0700
    Adding row div around two col-md-6 divs so it displays correctly on Chrome. Also fixed some broken style statements. refs #23542
  • lines changed 19, context: html, text, full: html, text
    a38f78deafbd07329f9a9cb2aeea4b77a7a288a4 Sat May 25 16:48:49 2019 -0700
    removing russia workshop - no visa! moving NHGRI to active list
• src/hg/hubApi/apiUtils.c
  • lines changed 6, context: html, text, full: html, text
    e310cad5467b2f306c8f90b23f749ad9f6a43296 Sat May 25 09:47:39 2019 -0700
    clean up argList processing code review refs #23521 #23427
• src/hg/hubApi/dataApi.h
  • lines changed 13, context: html, text, full: html, text
    e310cad5467b2f306c8f90b23f749ad9f6a43296 Sat May 25 09:47:39 2019 -0700
    clean up argList processing code review refs #23521 #23427
• src/hg/hubApi/getData.c
  • lines changed 6, context: html, text, full: html, text
    65bab3c27c40f988621003b34a72bc873d124d22 Tue May 21 16:20:34 2019 -0700
    need to return data in order by chromStart to allow fetching all track data with maxItemLimit interferrence refs #18869
  • lines changed 2, context: html, text, full: html, text
    e310cad5467b2f306c8f90b23f749ad9f6a43296 Sat May 25 09:47:39 2019 -0700
    clean up argList processing code review refs #23521 #23427
• src/hg/hubApi/hubApi.c
  • lines changed 8, context: html, text, full: html, text
    e310cad5467b2f306c8f90b23f749ad9f6a43296 Sat May 25 09:47:39 2019 -0700
    clean up argList processing code review refs #23521 #23427
• src/hg/hubApi/list.c
  • lines changed 4, context: html, text, full: html, text
    02d902f77c4015d68b551ed71c90b2c70be02447 Thu May 23 14:03:52 2019 -0700
    indicate parent of parent when two levels deep and trackLeavesOnly refs #18869
  • lines changed 5, context: html, text, full: html, text
    e310cad5467b2f306c8f90b23f749ad9f6a43296 Sat May 25 09:47:39 2019 -0700
    clean up argList processing code review refs #23521 #23427
• src/hg/hubApi/tests/expected/list03.gz
  • lines changed 0, context: html, text, full: html, text
    02d902f77c4015d68b551ed71c90b2c70be02447 Thu May 23 14:03:52 2019 -0700
    indicate parent of parent when two levels deep and trackLeavesOnly refs #18869
  • lines changed 0, context: html, text, full: html, text
    e289e0a17f783f7af53d94d6e0d0ff839a42058e Sat May 25 09:49:34 2019 -0700
    changing tables are going to be difficult to keep up with no redmine
• src/hg/hubApi/tests/expected/list09.gz
  • lines changed 0, context: html, text, full: html, text
    02d902f77c4015d68b551ed71c90b2c70be02447 Thu May 23 14:03:52 2019 -0700
    indicate parent of parent when two levels deep and trackLeavesOnly refs #18869
  • lines changed 0, context: html, text, full: html, text
    e289e0a17f783f7af53d94d6e0d0ff839a42058e Sat May 25 09:49:34 2019 -0700
    changing tables are going to be difficult to keep up with no redmine
• src/hg/hubApi/tests/expected/test26.gz
  • lines changed 0, context: html, text, full: html, text
    11cc9f40543e578113429ea48d1d3cdf858cae67 Tue May 21 17:02:41 2019 -0700
    add trackDump option for proof of concept refs #18869
• src/hg/hubApi/tests/expected/test27.gz
  • lines changed 0, context: html, text, full: html, text
    11cc9f40543e578113429ea48d1d3cdf858cae67 Tue May 21 17:02:41 2019 -0700
    add trackDump option for proof of concept refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 97, context: html, text, full: html, text
    29781ccf5a802932426ff9e78b5f191b4ebef5c0 Tue May 21 17:02:06 2019 -0700
    add trackDump option for proof of concept refs #18869
  • lines changed 3, context: html, text, full: html, text
    176827aa12f13df2c5dd10c0e5169504ab4f12ac Tue May 21 17:04:36 2019 -0700
    need forward declaration refs #18869
• src/hg/inc/encode/wgEncodeGencodeGeneSymbol.h
  • lines changed 2, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/inc/hui.h
  • lines changed 12, context: html, text, full: html, text
    58e020e2059bc60516a8c7282781a4201be42e70 Fri May 24 14:57:10 2019 -0700
    hubCheck reports errors in sortOrder setting of composite subtracks, refs #13428
• src/hg/lib/customFactory.c
  • lines changed 3, context: html, text, full: html, text
    cc91854c275763be567dd246d23336660dea58a0 Wed May 22 12:25:00 2019 -0700
    Adding hg.conf setting sessionDataDirOld so that isValidBigDataUrl won't complain about absolute paths of trashCleaner-saved files from old sessions. refs #22440
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.as
  • lines changed 1, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.c
  • lines changed 11, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.sql
  • lines changed 2, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/lib/hui.c
  • lines changed 9, context: html, text, full: html, text
    58e020e2059bc60516a8c7282781a4201be42e70 Fri May 24 14:57:10 2019 -0700
    hubCheck reports errors in sortOrder setting of composite subtracks, refs #13428
  • lines changed 16, context: html, text, full: html, text
    c29d92c458b3d21a19caf72954b91e949bf72886 Fri May 24 16:17:22 2019 -0700
    Fixing segfault in subtrack table printing for composite tracks with a sortOrder but no subgroups or missing subgroups, refs #23556
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 32, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
  • lines changed 1, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/makeDb/doc/mm10.txt
  • lines changed 41, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
  • lines changed 4, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 8, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
  • lines changed 6, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/makeDb/schema/all.joiner
  • lines changed 193, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    bc39e114d1cc62e9292797a95791163d2b1f3a1e Thu May 23 10:23:30 2019 -0700
    Changing priority and visibilities for bab00n #20769
  • lines changed 4, context: html, text, full: html, text
    fcee80f05ac950d02f1fc88212375a4c6f2f520d Thu May 23 11:46:07 2019 -0700
    Re-hiding chain track, it increased the load time of chr1 on dense by 30s #20769
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    2b054c4f759e6da89279e9ad43bf9929ee2b6573 Wed May 22 14:14:28 2019 -0700
    Changing default tracks for Chinese Hamster assemblies #23541, #23030
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    2b054c4f759e6da89279e9ad43bf9929ee2b6573 Wed May 22 14:14:28 2019 -0700
    Changing default tracks for Chinese Hamster assemblies #23541, #23030
• src/hg/makeDb/trackDb/criGri/criGriChoV2/description.html
  • lines changed 1, context: html, text, full: html, text
    2b054c4f759e6da89279e9ad43bf9929ee2b6573 Wed May 22 14:14:28 2019 -0700
    Changing default tracks for Chinese Hamster assemblies #23541, #23030
• src/hg/makeDb/trackDb/criGri/criGriChoV2/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    11ce2657a2e83a91cbf881e7601208e60c2ecd0d Tue May 21 11:33:24 2019 -0700
    Modifying default tracks for ChoV2 assembly #20540
• src/hg/makeDb/trackDb/fugu/gap.html
  • lines changed 1, context: html, text, full: html, text
    f8f3947eb9f2a6827713dd266a49d7a4659285c1 Wed May 22 09:45:10 2019 -0700
    Updating http to https for fr1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/affyTxnPhase3Super.html
  • lines changed 2, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/bipolar.html
  • lines changed 3, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/encTfChipPk.html
  • lines changed 2, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Sig.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Sites.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html
  • lines changed 2, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/hapmapLdPh.html
  • lines changed 2, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld5.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld6.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    12190c01d47cf5aa97b89af2845b2aa94953dac9 Tue May 21 09:46:09 2019 -0700
    removing trackDb.wgEncode.ra stanza for hg19, hg38. It will be easier to find release tags now, refs #21139
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.html
  • lines changed 20, context: html, text, full: html, text
    f1606c856af3725cfb36c551ca3167face4be69f Mon May 20 14:48:16 2019 -0700
    fix up gdcCancer html and ra
  • lines changed 37, context: html, text, full: html, text
    f1cc8edf4fad7ff103770c172c8d35491c0e22f1 Wed May 22 15:35:22 2019 -0700
    Making the HTML page conform to our standards, refs #22742
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra
  • lines changed 36, context: html, text, full: html, text
    f1606c856af3725cfb36c551ca3167face4be69f Mon May 20 14:48:16 2019 -0700
    fix up gdcCancer html and ra
• src/hg/makeDb/trackDb/human/hg38/knownGeneOld8.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    12190c01d47cf5aa97b89af2845b2aa94953dac9 Tue May 21 09:46:09 2019 -0700
    removing trackDb.wgEncode.ra stanza for hg19, hg38. It will be easier to find release tags now, refs #21139
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV31.html
  • lines changed 47, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV31.ra
  • lines changed 286, context: html, text, full: html, text
    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/makeDb/trackDb/human/humMusL.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/kiddEichlerValid.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/snp150Common.html
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    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/human/snp151Common.html
  • lines changed 1, context: html, text, full: html, text
    6254a2f3273acb0889ba875ffab273f0099cea16 Tue May 21 00:17:23 2019 -0700
    Fixe problems found by htmlCheck validate and hgNearTest robot
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM22.html
  • lines changed 30, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM22.ra
  • lines changed 286, context: html, text, full: html, text
    0df7d8fdb7c40a393e33791956a8c98ab460dead Thu May 23 10:54:50 2019 -0700
    import mouse GENCODE VM22 pre-release
• src/hg/near/hgNear/hgNearData/C_elegans/kimLifeCycleFull.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/C_elegans/kimLifeCycleMedian.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/D_melanogaster/arbLifeCycle.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/HInv.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/affyHumanExon.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/affyHumanExonDistance.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/expAll.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/expDense.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/gladHumES.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/gnfHumanAtlas2.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/gnfU95.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/gtex.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Human/humanNormal.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Mouse/gnfMouseAtlas2.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Mouse/gnfMouseAtlas3.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Mouse/gnfU74a.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Mouse/gnfU74b.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Mouse/gnfU74c.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Mouse/mouseLandscape.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Rat/gnfAtlas2.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/Rat/rn4/gnfAtlas2RgdGene2.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/S_cerevisiae/yeastChoCellCycle.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/affyExonTissuesGs.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/affyExonTissuesGsDistance.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/geneCategory.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/proteinAcc.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/near/hgNear/hgNearData/proteinName.html
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    583e30e3cbfc3c95eb94696d51c8979493caa9a3 Mon May 20 23:49:34 2019 -0700
    html pages fixed for problems found with htmlCheck validate and strictTagNestCheck
• src/hg/utils/hubCheck/hubCheck.c
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    29a7cfbfd306107b73c8c50c719fec2dc3807672 Tue May 21 12:30:04 2019 -0700
    Fixing bug I introduced in hubCheck found by MarkD, refs #23511
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    58e020e2059bc60516a8c7282781a4201be42e70 Fri May 24 14:57:10 2019 -0700
    hubCheck reports errors in sortOrder setting of composite subtracks, refs #13428
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
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    d8a632950a717f3ecaddbfb01c0e0b84f5b6726a Tue May 21 11:57:36 2019 -0700
    remove static limit on size the number of blocks that can be in a bigPsl. Test case not checked in, as it is 20mb for one record (fixes #23537)
• src/hg/utils/refSeqGet/tests/expected/basicListTest.gp
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/basicListTest.psl
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/basicListTest.rna.fa
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.gp
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.psl
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.rna.fa
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/hg/utils/refSeqGet/tests/input/versioned.acc
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    c260b871d385d446347ea0cf4fa2795111e28ae4 Fri May 24 14:08:36 2019 -0700
    RefSeq updated NM_153758.2 to NM_153758.3; update refSeqGet test files accordingly.
• src/lib/bPlusTree.c
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    607c224716976855955947c30bb6e525d0c79daa Wed May 22 10:27:40 2019 -0700
    check in a fix that Daniel Zerbino made to keep offsets in 64 bit land rather than casting them down to shorts
• src/lib/htmlPage.c
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    139f6e6d3044cb8fb0b7f7da6574acbd86603ca8 Thu May 23 16:14:09 2019 -0700
    whitespace fix
• src/utils/bamToPsl/bamToPsl.c
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    5232e16c9a3702b32078e2e665c3e2a9ffb1d696 Mon May 20 10:23:37 2019 -0700
    Fixing indentation, no refs
• src/utils/makefile
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    7c374ad903a137e9800c1e08acc0b1da357971dc Thu May 23 06:49:48 2019 -0700
    adding tdbSort and tdbRename to user apps, suggested by Kate, no redmine
• src/utils/pq
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    7c374ad903a137e9800c1e08acc0b1da357971dc Thu May 23 06:49:48 2019 -0700
    adding tdbSort and tdbRename to user apps, suggested by Kate, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    1c773e8388fccef579049c6def5c821a1b727700 Mon May 27 10:50:30 2019 -0700
    v383 preview1, refs #TICKETNUM
• src/utils/qa/weeklybld/summaryEmail.sh
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    861670e01c22c8ecabcf41cdfedb2da40f93b22d Mon May 20 17:49:26 2019 -0700
    Changing mention of Ann to mention Brian in summaryEmail.sh sent in code summaries

• lines changed: 2346
• files changed: 136