All File Changes

v382_preview2 to v382_base (2019-05-13 to 2019-05-20) v382

• confs/asia.hg.conf
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    0a82be6e02efea2c3cf896a624ffde046f05a92e Sun May 19 01:11:44 2019 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    0a82be6e02efea2c3cf896a624ffde046f05a92e Sun May 19 01:11:44 2019 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    0a82be6e02efea2c3cf896a624ffde046f05a92e Sun May 19 01:11:44 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/lib/cdwPageFooter.h
  • lines changed 4, context: html, text, full: html, text
    aafa7ad29c13b0c70205d79639cdedd64f03f827 Fri May 17 23:46:05 2019 -0700
    making relative links work for cdw CGIs (except cdwGetFile which is a special case.)
• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 1, context: html, text, full: html, text
    aafa7ad29c13b0c70205d79639cdedd64f03f827 Fri May 17 23:46:05 2019 -0700
    making relative links work for cdw CGIs (except cdwGetFile which is a special case.)
• src/hg/cirm/gateway/htdocs/README
  • lines changed 93, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/bestPractices.html
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    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 21, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 6, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 5, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/cescg/setRoot.html
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    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/dcg/brainOfCells.html
  • lines changed 5, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/dcg/heartOfCells.html
  • lines changed 5, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/dcg/setRoot.html
  • lines changed 5, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 6, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/help/cirmFAQ.html
  • lines changed 6, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/help/setRoot.html
  • lines changed 5, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 3, context: html, text, full: html, text
    12fa63959b4bf231fb0930befe0f34a45f55e3e8 Mon May 13 15:26:41 2019 -0700
    removing unneeded footer .. prefix
  • lines changed 4, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 15, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 5, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 25, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/setRoot.html
  • lines changed 4, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 17, context: html, text, full: html, text
    61769930f20061774aa09945aaaaf548ca349cd2 Sat May 18 00:47:44 2019 -0700
    Changing CIRM SSI to use new setRoot approach
• src/hg/das/README
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    9a9c276df329180208cfae36510f268bce72dccf Thu May 16 11:08:31 2019 -0700
    add note about moved URL for spec document no redmine
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    521dad5888fde0e10237c9c6b741e071cd0c5cee Tue May 14 09:47:56 2019 -0700
    hgSession: added CGI param hgS_sessionDataDbSuffix to randomize choice of customData db* when bulk-converting old saved sessions to use sessionDataDir/sessionDataDbPrefix. refs #22440
• src/hg/hgSession/hgSession.h
  • lines changed 6, context: html, text, full: html, text
    521dad5888fde0e10237c9c6b741e071cd0c5cee Tue May 14 09:47:56 2019 -0700
    hgSession: added CGI param hgS_sessionDataDbSuffix to randomize choice of customData db* when bulk-converting old saved sessions to use sessionDataDir/sessionDataDbPrefix. refs #22440
• src/hg/hgSession/sessionData.c
  • lines changed 34, context: html, text, full: html, text
    521dad5888fde0e10237c9c6b741e071cd0c5cee Tue May 14 09:47:56 2019 -0700
    hgSession: added CGI param hgS_sessionDataDbSuffix to randomize choice of customData db* when bulk-converting old saved sessions to use sessionDataDir/sessionDataDbPrefix. refs #22440
  • lines changed 26, context: html, text, full: html, text
    8b8805e978d9f3082c09351ee19bbad1ca09cac2 Tue May 14 10:38:44 2019 -0700
    When saving a session, if a table is not in customTrash then check whether it has already been saved to a customData* db. If not, just move on instead of aborting. refs #22440
  • lines changed 4, context: html, text, full: html, text
    e6254f8ad3cfeba60c7d09513ed6d560af47a5e0 Tue May 14 11:29:09 2019 -0700
    When saving a session, if hgPcrResult trash files are lost and removed from the cart var value, remove the cart var to prevent hgTracks from errAborting about bad cart var format. refs #22440
  • lines changed 1, context: html, text, full: html, text
    28d8f6e18b5c04a6f517bbb05e6a15d80f042dd9 Tue May 14 12:34:10 2019 -0700
    When saving a session, even if a ctfile or customComposite is already a symlink, scan it anyway in case it is an old session that points to customTrash db tables. refs #22440
  • lines changed 13, context: html, text, full: html, text
    94b3342ec1b9abe3993347c967b652f2e91ecf57 Thu May 16 12:18:49 2019 -0700
    When saving a trash path that is already a link, if it is a relative link (e.g. to ../../userdata/ct/xyz) then resolve it to a full path. refs #22440
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    16abd75370edf554ece294a4ae81047813a24a13 Mon May 13 15:29:38 2019 -0700
    make bigLolly packabale
  • lines changed 6, context: html, text, full: html, text
    a00c068d76b7c6c65d98ed95864171a8dfac75ef Fri May 17 13:28:02 2019 -0700
    Fix poorly behaving UI checkboxes (broken on previous purported cleanup. refs #23507
• src/hg/hgTracks/bigWarn.c
  • lines changed 4, context: html, text, full: html, text
    2093b34d5abc0f995acd69d28f83a60afaa3f966 Wed May 15 17:11:04 2019 -0700
    Prevent bigWarn methods from crashing if given a NULL or empty error message. refs #22440 note 130
• src/hg/hgTracks/hicTrack.c
  • lines changed 49, context: html, text, full: html, text
    3003dd8639adc83e45ead18a948ab7e168e9e6cc Mon May 20 08:11:37 2019 -0700
    More changes in response to code review, refs #23481
• src/hg/hgTracks/lolly.h
  • lines changed 1, context: html, text, full: html, text
    73aafeecdf0c78ad805ff7336fbece2abbe1fdd5 Mon May 13 17:20:30 2019 -0700
    fix a bug with squish and multi-region
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    8a28bf4166662fa7fdde5975bb42963aa55537cd Fri May 17 14:18:19 2019 -0700
    change variable names in response to code review
• src/hg/hgTracks/lollyTrack.c
  • lines changed 2, context: html, text, full: html, text
    73aafeecdf0c78ad805ff7336fbece2abbe1fdd5 Mon May 13 17:20:30 2019 -0700
    fix a bug with squish and multi-region
  • lines changed 2, context: html, text, full: html, text
    2424c1937ada0fcaf1cd250108af48b77a59e021 Thu May 16 19:46:33 2019 -0700
    some tweaks to lollipops
  • lines changed 1, context: html, text, full: html, text
    b13f98ae7240ac24c3a1c333a003899c84d9171d Thu May 16 19:58:25 2019 -0700
    don't draw outlines in lolly squish mode
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    8a28bf4166662fa7fdde5975bb42963aa55537cd Fri May 17 14:18:19 2019 -0700
    change variable names in response to code review
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    16abd75370edf554ece294a4ae81047813a24a13 Mon May 13 15:29:38 2019 -0700
    make bigLolly packabale
• src/hg/hgTracks/vcfTrack.c
  • lines changed 9, context: html, text, full: html, text
    e9d2ca4c5a20a3ce7ffe2aca7b55b0d010ca7ce4 Wed May 15 17:11:34 2019 -0700
    Don't fail silently when unable to open VCF. refs #22440 note 130
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 2, context: html, text, full: html, text
    82bc7657d57393c3e67c445dc5bf91102e6eb22f Mon May 20 08:13:40 2019 -0700
    remove warning message from R code that happens only on the most recent R version that is installed on the RR, refs #23024
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 13, context: html, text, full: html, text
    8185d253cdfd94afeef826febda5116c29fb80d8 Mon May 13 15:13:04 2019 -0700
    Adding a short new FAQ for restricted downloads and cleaning up some tag and link problems found by htmlCheck validate/checkLinks refs #23493
  • lines changed 1, context: html, text, full: html, text
    06e0c32c59ef43c97f035f6ee07397a7527bd135 Mon May 13 15:18:08 2019 -0700
    New FAQ for restricted downloads refs #23493
  • lines changed 5, context: html, text, full: html, text
    2ab7be34062f5565b9999da21272483260300933 Tue May 14 15:27:03 2019 -0700
    Adding a note about 404 from restricted data in the API in new FAQ and sharing genome-www email.
  • lines changed 1, context: html, text, full: html, text
    a966cf08fad9018e21921f1f34c70e4b36e5b8b6 Wed May 15 14:40:05 2019 -0700
    correct error code reference for protected data 404->403 refs #18869
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    eee0b1f73f5f01866f9e8b8dbb5ed153298d2638 Wed May 15 14:53:53 2019 -0700
    Linking to new hubAPI page from different FAQs #18869
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 8, context: html, text, full: html, text
    5c20012735003a09af722339a7ea57f5cb827066 Mon May 13 14:59:08 2019 -0700
    Commiting minor changes for code review #23486, also adding more param lines to customTrack text #23459
  • lines changed 4, context: html, text, full: html, text
    d05f4c65d4ba9e4b23b09d79567fe74d5ed2f9a0 Tue May 14 13:44:55 2019 -0700
    Removing & signs for consistency #23131
  • lines changed 19, context: html, text, full: html, text
    8ecb88fe6cfaf545b9d4e1eb67fd15cf5cb8ba72 Tue May 14 15:09:17 2019 -0700
    Made <input> format consistent, removed &s #23131
• src/hg/htdocs/FAQ/FAQreleases.html
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    be0654f589bf91075ae410aa09c6d2d1a0189d8a Fri May 17 14:51:36 2019 -0700
    adding felCat9 to credits and FAQreleases.html, refs #21043
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 21, context: html, text, full: html, text
    be0654f589bf91075ae410aa09c6d2d1a0189d8a Fri May 17 14:51:36 2019 -0700
    adding felCat9 to credits and FAQreleases.html, refs #21043
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    9111c13adfed0887d362f2992cf8cc5d8ea2b4f0 Fri May 17 15:39:05 2019 -0700
    editing text on felCat9 section on credits.html, refs #21043
  • lines changed 5, context: html, text, full: html, text
    35f432fe188901ce2db1cea26c3f0d420c4c42ac Mon May 20 10:12:03 2019 -0700
    Removing some dead links and updating a redirect, no RM
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 2, context: html, text, full: html, text
    e398bb02616f4bf19a03fc686f936fc36e50125a Mon May 13 15:58:19 2019 -0700
    Changing some examples for API #18869
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    3d50e0f18a7c64a85cd2dce1440f59ab0ee08ed7 Tue May 14 21:54:51 2019 -0700
    until this page becomes smart with js make the examples go explicitly to api.genome.ucsc.edu refs #18869
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    43156046fa4f7e34065194cb742ec39a4a7334e2 Wed May 15 10:44:07 2019 -0700
    Switching examples from plant to mouse hub and switching ce11 or hg38 #18869
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    064d15be8d0a3750a8cd30ea9b5523728c3d6528 Wed May 15 10:56:53 2019 -0700
    Adding additional API error examples #18869
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    50d394c587526db4622320a27d85f1e1ef8b9e4f Thu May 16 11:12:37 2019 -0700
    Adding an additional section with longer examples to api.html #18869
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    f33e484c4ccf75d8c34fde7c52d84d0299026a0d Thu May 16 15:47:51 2019 -0700
    Adding additional example to api #18869
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    6a2563095fd31472040d16eae2b2527945767f07 Thu May 16 16:46:08 2019 -0700
    Some missing anchor closings found by htmlCheck strictTagNestCheck
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    ae88abbaeb5f248692b8610e717d80988e600ce8 Fri May 17 09:56:55 2019 -0700
    Little fixes to api.html examples #18866
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 15, context: html, text, full: html, text
    5c20012735003a09af722339a7ea57f5cb827066 Mon May 13 14:59:08 2019 -0700
    Commiting minor changes for code review #23486, also adding more param lines to customTrack text #23459
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    eee0b1f73f5f01866f9e8b8dbb5ed153298d2638 Wed May 15 14:53:53 2019 -0700
    Linking to new hubAPI page from different FAQs #18869
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
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    8999273deebb9514bab0282c96011acb4355ecbd Fri May 17 13:25:31 2019 -0700
    Simplifying hgVai documentation disclaimer that it's not for medical use.
• src/hg/htdocs/goldenPath/help/interact.html
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    3a608ab4a201533404957194219bc57f9b5a40c4 Wed May 15 12:11:20 2019 -0700
    Updating interact example after getting blessing from Kate
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    9d3c7912849101bf5e1323cffc28a951a542245f Wed May 15 15:13:13 2019 -0700
    Updating interact example running by Kate
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    43efb3af4a3efe8d5f5b8e8a4e8464337a75790c Thu May 16 14:54:20 2019 -0700
    Updating interact help page to show interactUp and correct useScore=on and add image refs #23299
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    a45eed27f6c88468204a738e2c8c6da278b61898 Thu May 16 15:06:49 2019 -0700
    Adjusting image and adding more description about the image of interactUp refs #23299
• src/hg/htdocs/goldenPath/newsarch.html
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    c6ea6107d350d9b35f795e9de1b6c4169ae2e48d Thu May 16 11:02:50 2019 -0700
    adding felCat9 to newsarch and indexNews, refs #21043
• src/hg/htdocs/images/interactExample3.png
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    43efb3af4a3efe8d5f5b8e8a4e8464337a75790c Thu May 16 14:54:20 2019 -0700
    Updating interact help page to show interactUp and correct useScore=on and add image refs #23299
• src/hg/htdocs/inc/globalNavBar.inc
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    1b23d9f5faffda6287912933d04112b5461b46be Wed May 15 10:04:22 2019 -0700
    Revert menu item for Cell Browser, to original (remove 'Single', added 2/6/19). Request by AnnZ. refs #22679
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    54fd52c6942b2db5ec81dd14fde7e4043b7ceafe Thu May 16 11:43:01 2019 -0700
    adding JSON API menu link to help page refs #18869
• src/hg/htdocs/indexNews.html
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    c6ea6107d350d9b35f795e9de1b6c4169ae2e48d Thu May 16 11:02:50 2019 -0700
    adding felCat9 to newsarch and indexNews, refs #21043
• src/hg/htdocs/singlecell.html
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    602a1b57a8de2305f98b3cc8a84650fd11fcc45d Tue May 14 05:32:00 2019 -0700
    changes to singlecell page, refs #22679
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    9993fd4b5c799d726d70b217eaef31bba20d8f2c Tue May 14 14:32:30 2019 +0200
    more fixes to single cell page, refs #22679
• src/hg/htdocs/training/index.html
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    0b139a437b5da26900aba43902b47b4f4013f84c Thu May 16 22:05:27 2019 -0700
    spelled further correctly. addded link to brazil workshop
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    ac007f47ccbc3448b0209c04d8f80ecdf3cae00d Mon May 20 07:00:59 2019 -0700
    removed madison workshop. moving brazil workshop into next-four list
• src/hg/hubApi/apiUtils.c
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    ffcb793749fe12db176c00c04c0bd0676cf76a4d Tue May 14 16:15:12 2019 -0700
    now indicating maxItemsOutput limit reached refs #18869
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    ae4d6b0988cc34e674209890007aa8b46381603e Thu May 16 14:31:45 2019 -0700
    now returning itemsReturned count for any getData track function refs #18869
• src/hg/hubApi/dataApi.h
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    ffb8a4e71db0a481b94cba10e3b2802c691af7be Mon May 13 14:47:40 2019 -0700
    adding error 403 Forbidden
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    ffcb793749fe12db176c00c04c0bd0676cf76a4d Tue May 14 16:15:12 2019 -0700
    now indicating maxItemsOutput limit reached refs #18869
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    32155e82446098f60455eb7dd236f3739b049983 Thu May 16 13:49:45 2019 -0700
    recommended code review refs #23437
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    ae4d6b0988cc34e674209890007aa8b46381603e Thu May 16 14:31:45 2019 -0700
    now returning itemsReturned count for any getData track function refs #18869
• src/hg/hubApi/getData.c
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    6fee91c9d0a6a9a3d9e3588e44ae92596a9aa9fb Mon May 13 14:37:27 2019 -0700
    recognizing the trackDb setting tableBrowser to avoid revealing protected data refs #18869
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    ffcb793749fe12db176c00c04c0bd0676cf76a4d Tue May 14 16:15:12 2019 -0700
    now indicating maxItemsOutput limit reached refs #18869
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    40412e28d89a9d0e8ec7cc61ce56c93c600161ea Wed May 15 14:47:38 2019 -0700
    include reference to documentation FAQ for protected data refs #18869
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    ae4d6b0988cc34e674209890007aa8b46381603e Thu May 16 14:31:45 2019 -0700
    now returning itemsReturned count for any getData track function refs #18869
• src/hg/hubApi/hubApi.c
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    316230834978cf23c7ae8199514283626819fa28 Mon May 13 14:15:21 2019 -0700
    keep protected data out of view refs #18869
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    ffcb793749fe12db176c00c04c0bd0676cf76a4d Tue May 14 16:15:12 2019 -0700
    now indicating maxItemsOutput limit reached refs #18869
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    ae4d6b0988cc34e674209890007aa8b46381603e Thu May 16 14:31:45 2019 -0700
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• src/hg/hubApi/list.c
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    6fee91c9d0a6a9a3d9e3588e44ae92596a9aa9fb Mon May 13 14:37:27 2019 -0700
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    af113249f30db748bae4c4c79cc270c548eb46d4 Tue May 14 14:13:29 2019 -0700
    now providing an itemCount for each track in the list tracks function refs #18869
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    add restricted data error test refs #18869
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• src/hg/hubApi/tests/expected/wig20.gz
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• src/hg/hubApi/tests/expected/wig22.gz
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• src/hg/hubApi/tests/expected/wig23.gz
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• src/hg/hubApi/tests/expected/wig24.gz
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• src/hg/hubApi/tests/jsonConsumer.pl
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    41041598ce79e1b299e5aba1a9b1e2fe41775d12 Thu May 16 11:27:11 2019 -0700
    reduce number of test servers refs #18869
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    fc0d65cb3b98202426346c555bfef1eb5bfacd1a Thu May 16 14:53:13 2019 -0700
    consolidate all the parameter passing into one spot refs #18869
• src/hg/hubApi/tests/makefile
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    1e64cd7af04589dcf62384be522455b1021eaecf Tue May 14 16:19:01 2019 -0700
    the Broad dog hub broke down refs #18869
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    4d1fcce80ce7b5c9391820136892970dcd975748 Wed May 15 15:09:09 2019 -0700
    add restricted data error test refs #18869
• src/hg/hubApi/tests/pythonClient.py
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    f50aa23023cbc478df90deaded10321b75349e8b Tue May 14 15:35:06 2019 -0700
    Fixup python client before adding to userapps, refs #18869
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    692b26d94a66f8c655dc65a2d4e697dcd500e5e8 Tue May 14 15:48:44 2019 -0700
    Adding python client to userapps, refs #18869
• src/hg/inc/hicUi.h
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    d7b8c8436b55a4f08f46a7caae8bf3ab88773f9f Fri May 17 13:40:41 2019 -0700
    Changes in response to code review, refs #23481
• src/hg/inc/versionInfo.h
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    cab37f8d9da4565b7c5bbbe643c0827e5581f2f7 Mon May 20 10:12:42 2019 -0700
    New version number v382
• src/hg/lib/clusterInputTrackTableEncode3Tfbs.as
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    61b98e84a58f8049465452e435fa9b6048777bf5 Thu May 16 11:52:43 2019 -0700
    Add track tables for ENCODE 3 TFBS Clusters track. refs #21139
• src/hg/lib/clusterInputTrackTableEncode3Tfbs.sql
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    61b98e84a58f8049465452e435fa9b6048777bf5 Thu May 16 11:52:43 2019 -0700
    Add track tables for ENCODE 3 TFBS Clusters track. refs #21139
• src/hg/lib/customTrack.c
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    5ab68cb3e725251bdcd2d9b835883af146f72dc7 Tue May 14 12:55:56 2019 -0700
    When loading custom tracks, if all have been removed then the ctfile_ var is also removed, so don't errAbort if it's gone.
• src/hg/lib/hic.c
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    d7b8c8436b55a4f08f46a7caae8bf3ab88773f9f Fri May 17 13:40:41 2019 -0700
    Changes in response to code review, refs #23481
• src/hg/lib/hicUi.c
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    d7b8c8436b55a4f08f46a7caae8bf3ab88773f9f Fri May 17 13:40:41 2019 -0700
    Changes in response to code review, refs #23481
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    3003dd8639adc83e45ead18a948ab7e168e9e6cc Mon May 20 08:11:37 2019 -0700
    More changes in response to code review, refs #23481
• src/hg/lib/hui.c
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    53e7415427718eb301c604850ae155d739c84bf7 Wed May 15 15:53:23 2019 -0700
    Removing useless warning. refs #23480
• src/hg/lib/straw/straw.cpp
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    efd356f3dc1b54a6801fdaffa9fc4d5e9d5d96f9 Mon May 13 13:42:39 2019 -0700
    Quick fix to avoid namespace collision, pending better handling of straw version numbers, refs #18842
• src/hg/liftAgp/liftAgp.c
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    ae0d467a80c1543026ccc2252ffd319b184e12d2 Thu May 16 11:28:07 2019 -0700
    improved warning messages no redmine
• src/hg/makeDb/doc/dm6/multiz124way.txt
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    79fb0cba806fd429dbd35caf21944d3e3b24a3d2 Thu May 16 11:28:45 2019 -0700
    note about index on Frames table no redmine
• src/hg/makeDb/doc/encode3/tfbs.txt
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
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    7b3269bd1e75158ddf049cd109f7f4e1383da0ec Tue May 14 10:36:23 2019 -0700
    Color subtracks by DNase similarity. refs #23243
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    17a0041ba1ccccb438ab59855538e53d0f78e0f9 Wed May 15 14:17:06 2019 -0700
    Final polish: 1. Set default on tracks. 2. Fix some uniqueness problems with shortLabels and colors.
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    61b98e84a58f8049465452e435fa9b6048777bf5 Thu May 16 11:52:43 2019 -0700
    Add track tables for ENCODE 3 TFBS Clusters track. refs #21139
• src/hg/makeDb/schema/all.joiner
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    61b98e84a58f8049465452e435fa9b6048777bf5 Thu May 16 11:52:43 2019 -0700
    Add track tables for ENCODE 3 TFBS Clusters track. refs #21139
• src/hg/makeDb/trackDb/crisprAll.html
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    623066b7ef5424f51400355a62706c2c5bc69283 Mon May 20 09:34:05 2019 -0700
    add html page for crisprAll track refs #23514
• src/hg/makeDb/trackDb/drosophila/chainApiMel2.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroAna1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroMoj1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroVir1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroYak1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevSignal.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevTransfrags.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/bacEndPairs.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements15way.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netApiMel2.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroAna1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroMoj1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroVir1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroYak1.html
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    52f01ca3a6d164a0e3b5b153e8d1a4ecb035e669 Thu May 16 08:48:06 2019 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
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    9bcf301f1667b1ad9639b3582befde9c3c6e29c1 Wed May 15 10:10:38 2019 -0700
    Updating http to https for eboVir3, uiLinks cronjob.
• src/hg/makeDb/trackDb/ebola/gireReferences.html
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    9bcf301f1667b1ad9639b3582befde9c3c6e29c1 Wed May 15 10:10:38 2019 -0700
    Updating http to https for eboVir3, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/clinvar.html
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    ba9b4bffc83af21310d6525f54d82bd117854c04 Wed May 15 16:33:39 2019 +0200
    improving data updates docs for clinvar, no redmine, just noticed this while using the track
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    c1072a276744b6c58f7f88b997c17eb6da489616 Wed May 15 07:38:12 2019 -0700
    another update to the clinvar docs page, no redmine
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    c21b2a99d811309db84934580b463d68a6cded86 Wed May 15 07:54:42 2019 -0700
    another small clinvar docs change, no redmine
• src/hg/makeDb/trackDb/human/encTfChipPk.html
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    5948426ec1f630f4aa6d40ec40b87ae6ad2a13fb Wed May 15 14:35:33 2019 -0700
    Add informational paragraph (JK request) and notes about subtrack coloring. refs #23243
• src/hg/makeDb/trackDb/human/hg19/encode3.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
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    c8f4a96b455efcc2a2c5cf0217244c438aeb9e23 Mon May 13 17:55:37 2019 -0700
    Add ENCODE 2 cell colors to tracks (affects about half the tracks). refs #23243
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    17a0041ba1ccccb438ab59855538e53d0f78e0f9 Wed May 15 14:17:06 2019 -0700
    Final polish: 1. Set default on tracks. 2. Fix some uniqueness problems with shortLabels and colors.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    b3dd838207a376eaf3182879d0246bc4311c1f9a Fri May 17 11:30:42 2019 -0700
    adding beta release tags for encode3.ra, refs #21139
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.dev.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.new.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.new.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
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    7b3269bd1e75158ddf049cd109f7f4e1383da0ec Tue May 14 10:36:23 2019 -0700
    Color subtracks by DNase similarity. refs #23243
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    17a0041ba1ccccb438ab59855538e53d0f78e0f9 Wed May 15 14:17:06 2019 -0700
    Final polish: 1. Set default on tracks. 2. Fix some uniqueness problems with shortLabels and colors.
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.html
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    d4bcf903ea90a74adba61248a68fc10ed28f6fee Tue May 14 03:24:02 2019 -0700
    fixes after code review, refs #23482
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra
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    16abd75370edf554ece294a4ae81047813a24a13 Mon May 13 15:29:38 2019 -0700
    make bigLolly packabale
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    b3dd838207a376eaf3182879d0246bc4311c1f9a Fri May 17 11:30:42 2019 -0700
    adding beta release tags for encode3.ra, refs #21139
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    c8b4b5ee8db9d49e0cc7c2cd49aa2a47ef87c5da Mon May 20 09:29:55 2019 -0700
    Added beta tag to trackDb.wgEncode.ra file and removed the include encode3.ra statement from the trackDb.ra file, refs #21139
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
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    c8b4b5ee8db9d49e0cc7c2cd49aa2a47ef87c5da Mon May 20 09:29:55 2019 -0700
    Added beta tag to trackDb.wgEncode.ra file and removed the include encode3.ra statement from the trackDb.ra file, refs #21139
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.dev.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.new.ra
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    5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b Mon May 13 16:53:13 2019 -0700
    Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139
• src/hg/makeDb/trackDb/mouse/mm10/tabulaMuris.html
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    89cd722b6825f1348bd4787b2f6dae9e6f3b7491 Tue May 14 03:24:53 2019 -0700
    fixing html page after code review, refs #23482
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
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    a3459250bfb6d65b264370225fc50568c1f84065 Tue May 14 02:11:48 2019 -0700
    fixing typo in cell name in tab. muris
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    50a03ec4455df9e10b785500b2de984c3452a966 Thu May 16 11:29:39 2019 -0700
    add chainNet for GRCm38B experiment no redmine
• src/hg/makeDb/trackDb/worm/caePb2/ctgPos2.html
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    f038fa1a386d9204ef4b90c8570ce65e8be17352 Tue May 14 09:02:38 2019 -0700
    Updating http to https for caePb2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/caePb2/gap.html
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    f038fa1a386d9204ef4b90c8570ce65e8be17352 Tue May 14 09:02:38 2019 -0700
    Updating http to https for caePb2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/caePb2/gold.html
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    f038fa1a386d9204ef4b90c8570ce65e8be17352 Tue May 14 09:02:38 2019 -0700
    Updating http to https for caePb2, uiLinks cronjob.
• src/hg/utils/hubCheck/hubCheck.c
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    fde90be0141f2a9f4ecbe31f394f05b10d2f03f3 Tue May 14 09:12:20 2019 -0700
    Moving the parents and children hub check into the hubCheck program, refs #13428
• src/hg/utils/jsonQuery/jsonQuery.c
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    9b45eef7290592e268733f18aaff0503cfa82d4a Mon May 13 12:08:31 2019 -0700
    jsonQuery: Use netLineFileOpen not lineFileOpen, to support URLs.
• src/inc/htmlPage.h
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    fa22e76fd69504695f343f51fdd8368050063ed6 Wed May 15 23:57:53 2019 -0700
    adding -withSrc option to htmlCheck commands getLinks checkLinks checkLinks2 checkLocalLinks checkLocalLinks2
• src/inc/obscure.h
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    d7b8c8436b55a4f08f46a7caae8bf3ab88773f9f Fri May 17 13:40:41 2019 -0700
    Changes in response to code review, refs #23481
• src/inc/srcVersion.h
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    cab37f8d9da4565b7c5bbbe643c0827e5581f2f7 Mon May 20 10:12:42 2019 -0700
    New version number v382
• src/lib/asParse.c
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    bf3fd9d0f863602da1ecd3b49f137e3515341c7b Thu May 16 16:33:00 2019 -0700
    allow BED itemRgb field to be name "itemRgb" instead of "reserved" fixes #23499
• src/lib/dystring.c
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    279df51388cf7da5474142bc74457f671c74b0ac Tue May 14 09:26:57 2019 -0700
    dyStringQuoteString needs to escape the escape character in addition to the quote character.
• src/lib/htmlPage.c
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    fa22e76fd69504695f343f51fdd8368050063ed6 Wed May 15 23:57:53 2019 -0700
    adding -withSrc option to htmlCheck commands getLinks checkLinks checkLinks2 checkLocalLinks checkLocalLinks2
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    f01299b4b6f140d82fb6ad08576b50823b47ff40 Thu May 16 22:08:12 2019 -0700
    Fixes a bug that happens if space appears before = after attribute name. Fixed it to strip out newlines from quoted attribute values which the standard supports for input but which are not actually part of attribute value, found in a very long url in cite.html. Also now make validate function check for two more illegal conditions: a space directly before the tag name which is illegal.
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    7d630742f6a1c185e80cf46abf5af0b704db1784 Fri May 17 23:41:18 2019 -0700
    Adding check that A tags are NOT nested. For htmlCheck.
• src/lib/obscure.c
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    d7b8c8436b55a4f08f46a7caae8bf3ab88773f9f Fri May 17 13:40:41 2019 -0700
    Changes in response to code review, refs #23481
• src/utils/bamToPsl/bamToPsl.c
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    447f4cc79938d078c168f9f7e65e7b1469681c7d Fri May 17 14:40:18 2019 -0700
    bamToPsl skips reads with the '*' cigar string, refs #23506
• src/utils/crisprKmers/crisprKmers.c
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    7173ec16f870dfd0a5ee590354fc604ecfcf1bc9 Thu May 16 11:30:42 2019 -0700
    correctly dumping guides no redmine
• src/utils/htmlCheck/htmlCheck.c
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    eeaec5caae169706b4945f25ff8caa92eac66813 Mon May 13 16:04:10 2019 -0700
    htmlCheck needs to support 303 because Nature magazine is using them now.
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    fa22e76fd69504695f343f51fdd8368050063ed6 Wed May 15 23:57:53 2019 -0700
    adding -withSrc option to htmlCheck commands getLinks checkLinks checkLinks2 checkLocalLinks checkLocalLinks2
• src/utils/makefile
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    692b26d94a66f8c655dc65a2d4e697dcd500e5e8 Tue May 14 15:48:44 2019 -0700
    Adding python client to userapps, refs #18869
• src/utils/qa/weeklybld/buildEnv.csh
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    0793cd0667685cd1dad0d6d431fbd9dc86a375d6 Mon May 20 10:11:59 2019 -0700
    v382 final build, refs #23326
• src/utils/qa/weeklybld/sendLogEmail.pl
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    e2210c09420d6cdfac88f9cbea58172fbeb1e236 Mon May 13 10:27:44 2019 -0700
    correct azweig email no redmine
• src/utils/ucscApiClient
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    692b26d94a66f8c655dc65a2d4e697dcd500e5e8 Tue May 14 15:48:44 2019 -0700
    Adding python client to userapps, refs #18869
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    88f34170f2ed2d1e755d3f617b17e34b0df5eda6 Wed May 15 11:12:11 2019 -0700
    Making python api client handle pipes a bit more gracefully
• src/weblet/bottleneck/bottleneck.c
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    711e4eb4e684dad38a67539691fbef21a9a3f8fa Thu May 16 11:35:18 2019 -0700
    reformat white space no code change no redmine

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