All File Changes

v388_preview to v388_preview2 (2019-09-09 to 2019-09-16) v388

• src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c
  • lines changed 69, context: html, text, full: html, text
    ff2d32fb46b3b97bcf6bf061ef0f8fd888556e64 Sun Sep 15 17:47:57 2019 -0700
    Making all the series.contact_ prefixed fields get expanded to have one item (blank alas except in case of contact_name) for all the contributors. This and the new tabToTabDir unroll type is enough to save the curators from a separate cut and paste for each person n the project, which can get tedious.
• src/hca/hcat/hcatParseParth/doTest.csh
  • lines changed 2, context: html, text, full: html, text
    b76d22919942bde7b254eb6155dd93f32b825437 Sun Sep 15 12:13:27 2019 -0700
    Saving some shell scripts that I'll probably use again though there's not much to them.
• src/hca/hcat/hcatParseParth/fetchAndParse.csh
  • lines changed 3, context: html, text, full: html, text
    b76d22919942bde7b254eb6155dd93f32b825437 Sun Sep 15 12:13:27 2019 -0700
    Saving some shell scripts that I'll probably use again though there's not much to them.
• src/hca/hcat/hcatParseParth/hcatParseParth.c
  • lines changed 275, context: html, text, full: html, text
    e28685060d11d006ed870d8b3030e251bb63076b Thu Sep 12 17:02:26 2019 -0700
    First commit of program to import JSON from Parth's tracker into hcat. Needs to generate table headers, but the table columns are looking good by visual inspection at least.
  • lines changed 31, context: html, text, full: html, text
    aea3d32ec26cf8d333ba7af1d27964addad961c4 Thu Sep 12 22:15:48 2019 -0700
    Produces header lines in the output files now. This version used to preload hcat with the older data, but not yet parsing out the status bits.
  • lines changed 83, context: html, text, full: html, text
    867a3f8e1801a5e150dcc054a9f8b7b05fe6f428 Sat Sep 14 14:34:55 2019 -0700
    Decided to go with a separate table for the tracker info since project was getting so big. No regrets!
• src/hca/hcat/hcatParseParth/makefile
  • lines changed 3, context: html, text, full: html, text
    e28685060d11d006ed870d8b3030e251bb63076b Thu Sep 12 17:02:26 2019 -0700
    First commit of program to import JSON from Parth's tracker into hcat. Needs to generate table headers, but the table columns are looking good by visual inspection at least.
• src/hca/hcat/hcatParseParth/testExpected/hcat_contributor.tsv
  • lines changed 64, context: html, text, full: html, text
    e28685060d11d006ed870d8b3030e251bb63076b Thu Sep 12 17:02:26 2019 -0700
    First commit of program to import JSON from Parth's tracker into hcat. Needs to generate table headers, but the table columns are looking good by visual inspection at least.
  • lines changed 65, context: html, text, full: html, text
    aea3d32ec26cf8d333ba7af1d27964addad961c4 Thu Sep 12 22:15:48 2019 -0700
    Produces header lines in the output files now. This version used to preload hcat with the older data, but not yet parsing out the status bits.
• src/hca/hcat/hcatParseParth/testExpected/hcat_project.tsv
  • lines changed 25, context: html, text, full: html, text
    e28685060d11d006ed870d8b3030e251bb63076b Thu Sep 12 17:02:26 2019 -0700
    First commit of program to import JSON from Parth's tracker into hcat. Needs to generate table headers, but the table columns are looking good by visual inspection at least.
  • lines changed 26, context: html, text, full: html, text
    aea3d32ec26cf8d333ba7af1d27964addad961c4 Thu Sep 12 22:15:48 2019 -0700
    Produces header lines in the output files now. This version used to preload hcat with the older data, but not yet parsing out the status bits.
• src/hca/hcat/hcatParseParth/testIn.json
  • lines changed 2473, context: html, text, full: html, text
    e28685060d11d006ed870d8b3030e251bb63076b Thu Sep 12 17:02:26 2019 -0700
    First commit of program to import JSON from Parth's tracker into hcat. Needs to generate table headers, but the table columns are looking good by visual inspection at least.
• src/hca/hcat/hcatParseParth/updateProd.csh
  • lines changed 4, context: html, text, full: html, text
    b76d22919942bde7b254eb6155dd93f32b825437 Sun Sep 15 12:13:27 2019 -0700
    Saving some shell scripts that I'll probably use again though there's not much to them.
• src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c
  • lines changed 11, context: html, text, full: html, text
    552331b42c93f88781b16183d733f9f48d07802f Fri Sep 6 14:05:56 2019 -0700
    dealing with change of project_role to be a foreign key into contributorType. Removing contact from lab until I figure out how to do it right. Fixed a lab_contributor mixup.
• src/hca/hcat/mysite/hcat/admin.py
  • lines changed 74, context: html, text, full: html, text
    3a16297829778f22d084827214ed1b6b650e866c Thu Sep 5 16:31:51 2019 -0700
    Making comments just text fields. Making wranglers, curators, and software developers as separate tables with a link to plain old contributors. A bunch of more minor changes that were easy to implement described in the 0.5 section of version.txt.
  • lines changed 14, context: html, text, full: html, text
    e61dee7bb39246a91885ef62078d45818559bedd Fri Sep 6 14:01:59 2019 -0700
    Switching date/deliverable order so lines up pretty. Changing some things in response to Paris's requests.
  • lines changed 1, context: html, text, full: html, text
    f75e51cbc8d0fa611902086582672ea627ab643f Thu Sep 12 22:20:45 2019 -0700
    Adding uuid field to project.
  • lines changed 7, context: html, text, full: html, text
    de60f72591d3d1dac467019d1cfc6e7a21edf31a Fri Sep 13 07:11:35 2019 -0700
    Got rid of search_fields that involve foreign keys or multis as they just crash Django.
  • lines changed 31, context: html, text, full: html, text
    efb20cbb23e6e1a8d09ef36c69c6367e86fcbb52 Sat Sep 14 14:36:30 2019 -0700
    New Tracker model and stuff to show it in the admin.
  • lines changed 1, context: html, text, full: html, text
    dd17da0c5dfbf9cf7e7aa4cde8fdc8ba14389663 Sun Sep 15 17:48:50 2019 -0700
    Showing submit_date instead of title. Looks cleaner and more informative.
• src/hca/hcat/mysite/hcat/models.py
  • lines changed 89, context: html, text, full: html, text
    3a16297829778f22d084827214ed1b6b650e866c Thu Sep 5 16:31:51 2019 -0700
    Making comments just text fields. Making wranglers, curators, and software developers as separate tables with a link to plain old contributors. A bunch of more minor changes that were easy to implement described in the 0.5 section of version.txt.
  • lines changed 25, context: html, text, full: html, text
    e61dee7bb39246a91885ef62078d45818559bedd Fri Sep 6 14:01:59 2019 -0700
    Switching date/deliverable order so lines up pretty. Changing some things in response to Paris's requests.
  • lines changed 2, context: html, text, full: html, text
    f75e51cbc8d0fa611902086582672ea627ab643f Thu Sep 12 22:20:45 2019 -0700
    Adding uuid field to project.
  • lines changed 23, context: html, text, full: html, text
    efb20cbb23e6e1a8d09ef36c69c6367e86fcbb52 Sat Sep 14 14:36:30 2019 -0700
    New Tracker model and stuff to show it in the admin.
• src/hca/hcat/mysite/hcat/urls.py
  • lines changed 4, context: html, text, full: html, text
    12f8b1f11a6bc0d7a9694a7b64163123f8ad3e8e Thu Sep 12 22:22:47 2019 -0700
    Starting to tinker on non-admin views.
• src/hca/hcat/mysite/hcat/views.py
  • lines changed 19, context: html, text, full: html, text
    12f8b1f11a6bc0d7a9694a7b64163123f8ad3e8e Thu Sep 12 22:22:47 2019 -0700
    Starting to tinker on non-admin views.
• src/hca/hcat/mysite/templates/admin/base_site.html
  • lines changed 2, context: html, text, full: html, text
    9caa48dc0a1f42140f778d262c7efadd506351e3 Thu Sep 12 22:23:36 2019 -0700
    Some renaming from HCAT to Tuatara.
  • lines changed 1, context: html, text, full: html, text
    52312aa9e2d2642c8ab02602f43941db285c1742 Sun Sep 15 17:49:41 2019 -0700
    Bumping visible version on dev site.
• src/hca/hcat/mysite/templates/hcat/project_detail.html
  • lines changed 2, context: html, text, full: html, text
    12f8b1f11a6bc0d7a9694a7b64163123f8ad3e8e Thu Sep 12 22:22:47 2019 -0700
    Starting to tinker on non-admin views.
• src/hca/hcat/mysite/templates/hcat/project_list.html
  • lines changed 9, context: html, text, full: html, text
    12f8b1f11a6bc0d7a9694a7b64163123f8ad3e8e Thu Sep 12 22:22:47 2019 -0700
    Starting to tinker on non-admin views.
• src/hca/hcat/mysite/versions.txt
  • lines changed 23, context: html, text, full: html, text
    0512731f08d36248257c4ed6682f1abdafcfee3b Thu Sep 5 16:27:50 2019 -0700
    Describing changes since last production release.
  • lines changed 3, context: html, text, full: html, text
    87b7cd26d44ee9fee02081c5ae0d346a19be2178 Fri Sep 6 13:40:00 2019 -0700
    Adding in descriptions of changes from Paris' requests.
  • lines changed 2, context: html, text, full: html, text
    a0ed68b1fddb7782e86481e27b972fa14caec97e Fri Sep 6 14:03:30 2019 -0700
    Recording latest mods.
  • lines changed 10, context: html, text, full: html, text
    f75e51cbc8d0fa611902086582672ea627ab643f Thu Sep 12 22:20:45 2019 -0700
    Adding uuid field to project.
  • lines changed 15, context: html, text, full: html, text
    96656d98549f8f0bb4ad2931330f35110ee8b857 Sat Sep 14 14:37:02 2019 -0700
    Documenting changes since last version.
• src/hg/hgCustom/hgCustom.c
  • lines changed 24, context: html, text, full: html, text
    832026164cc5f13b2764e5556bf003864d662938 Mon Sep 9 14:19:33 2019 -0700
    now allowing hgCustom to play the bottleneck game, and bold highlight the error 429 message refs #23217
  • lines changed 1, context: html, text, full: html, text
    64892522148b1d3ef907e319e1b81c2f5862459d Mon Sep 9 14:33:20 2019 -0700
    correctly use the name hgCustom in the earlyBotCheck() call refs #23217
  • lines changed 3, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/hgGateway/hgGateway.c
  • lines changed 11, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
  • lines changed 24, context: html, text, full: html, text
    74c99d39c800193f07a881ce98ee4b7065cee6dc Fri Sep 13 10:00:57 2019 -0700
    get the warning message out of the warning only message to be used elsewhere and add measureTiming printout to hgGateway refs #23217
• src/hg/hgSession/hgSession.c
  • lines changed 6, context: html, text, full: html, text
    cd8473cd35938a2831c33c2885434cccadcf0376 Tue Sep 10 11:57:53 2019 -0700
    When re-saving a session, don't delete the session from namedSessionDb until & unless saveSessionData has completed without errAbort. By deleting before saveSessionData, we were losing sessions when there was an errAbort condition. refs #24119
  • lines changed 1, context: html, text, full: html, text
    6768497aef1c95abb9b086299377cd09a9bc6c72 Wed Sep 11 11:23:14 2019 -0700
    Specifically for re-saving an existing session (to convert from trash/customTrash to userdata/customData*), don't trimSpaces from the sessionName, in order to support old sessions with encoded spaces at the beginning or end of sessionName.
  • lines changed 1, context: html, text, full: html, text
    74712c66fa53216d421fb68e6b643d3f2182271a Wed Sep 11 13:37:46 2019 -0700
    Strip leading/trailing spaces from session name when changing session name, not only when saving a session the usual way. refs #24124
  • lines changed 88, context: html, text, full: html, text
    a8787479d4851e364fa680e19d68fe5743b096be Thu Sep 12 13:10:19 2019 -0700
    When changing session name, detect if the new name would overwrite an existing session and confirm with user. Then allow overwrite if confirmed. refs #24133
  • lines changed 6, context: html, text, full: html, text
    c8df7c4f49ddb9af903603586ad4238159318942 Fri Sep 13 10:41:26 2019 -0700
    The session details 'use' button also has the effect of accepting changes (ugh), so check if a name change means overwriting an existing session there too. refs #24133
  • lines changed 10, context: html, text, full: html, text
    fb59b3cbfd52ccb31b7691e1718a23fdad4c9e9f Fri Sep 13 11:16:17 2019 -0700
    Removed the redundant and troublesome 'use' and 'delete' buttons from the session details change form. refs #24133
• src/hg/hgSession/sessionData.c
  • lines changed 7, context: html, text, full: html, text
    d068d2fb67acf09e2b8b333a32c099da418a8df9 Tue Sep 10 14:12:30 2019 -0700
    When re-saving a session, if userdata ctfile already exists, just recreate it instead of errAborting; otherwise, the session can never be saved after an initial timeout or other problem. refs #24121.
  • lines changed 3, context: html, text, full: html, text
    196f6933bbd781e74d3d63203b7d6d4ad3ad6eac Tue Sep 10 14:39:42 2019 -0700
    Add NULL check in case a customTrash wiggle table has no rows. I haven't found a way to recreate an empty wiggle table with the CGIs, only manually, but there was one case of this in the >100,000 old sessions on the RR.
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    cdae2fc61c0a4e03c2dee7321c91a42aa1ebdfc0 Mon Sep 9 15:43:17 2019 -0700
    now getting hgTables into the earlyBotCheck() game and fixup earlyBotCheck() to honor the exception list and default to a delay fraction value of 1.0 refs #23217
  • lines changed 3, context: html, text, full: html, text
    ca3f45c0d7c8ea372d9202eb5160c0f9268c95f2 Wed Sep 11 10:38:12 2019 -0700
    use the correct default delay fraction refs #23217
  • lines changed 1, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/hgTables/hic.c
  • lines changed 6, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    af461ddaef211c16a3ca52913df3f4c9a95ed48d Thu Sep 12 13:38:55 2019 -0700
    Extend labelOnFeature setting to support dense mode w/o labels (as usual in our tracks). Using this feature in chromatin state tracks. refs #24128
  • lines changed 2, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/hgTracks/hicTrack.c
  • lines changed 25, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/hgTracks/renderMain.c
  • lines changed 1, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/hgTracks/simpleTracks.c
  • lines changed 13, context: html, text, full: html, text
    af461ddaef211c16a3ca52913df3f4c9a95ed48d Thu Sep 12 13:38:55 2019 -0700
    Extend labelOnFeature setting to support dense mode w/o labels (as usual in our tracks). Using this feature in chromatin state tracks. refs #24128
• src/hg/hgc/interactClick.c
  • lines changed 21, context: html, text, full: html, text
    601ece4d47e590855e1232bc968593299fc4b703 Wed Sep 11 11:09:09 2019 -0700
    Clean up and expand interactMultiRegion trackDb seetting to specify padding. Needed for transEqtl (huge and chross-chrom interactions). refs #24037
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 7, context: html, text, full: html, text
    7835eff52a5b920e2ab64123fa72d1faf8f288f5 Fri Sep 13 14:46:35 2019 -0700
    fixing two small bits
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 6, context: html, text, full: html, text
    e2fa282b77b041b4acbdfb4644706c45828a2889 Thu Sep 12 15:31:24 2019 -0700
    Linking to resources from chromEnd in BED FAQ format after MLQ email refs #24126
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 10, context: html, text, full: html, text
    e2f1d4f8b6309f36a64c62fd87a85434811b05f3 Tue Sep 10 09:33:46 2019 -0700
    Adding hard link to save users 1 command in bedToBigBed conversion #24092
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 24, context: html, text, full: html, text
    eeb045a2a436539a1a8797984dfe7dfcaacf789d Wed Sep 11 17:09:15 2019 -0700
    Putting ASHG poster information into the interact.html help page
• src/hg/htdocs/images/interactUnderstanding1.png
  • lines changed 0, context: html, text, full: html, text
    eeb045a2a436539a1a8797984dfe7dfcaacf789d Wed Sep 11 17:09:15 2019 -0700
    Putting ASHG poster information into the interact.html help page
• src/hg/htdocs/images/interactUnderstanding2.png
  • lines changed 0, context: html, text, full: html, text
    eeb045a2a436539a1a8797984dfe7dfcaacf789d Wed Sep 11 17:09:15 2019 -0700
    Putting ASHG poster information into the interact.html help page
• src/hg/htdocs/style/HGStyle.css
  • lines changed 39, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/htdocs/training/index.html
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    92b799351a6261ff7622821855634b7e0a4ac887 Mon Sep 9 14:21:51 2019 -0700
    added better, direct link to ashg workshop
• src/hg/inc/Cstraw.h
  • lines changed 1, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/inc/botDelay.h
  • lines changed 5, context: html, text, full: html, text
    2c0d72680e3e008b31cc5946435d4ec8a8657e05 Thu Sep 12 14:24:08 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
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    74c99d39c800193f07a881ce98ee4b7065cee6dc Fri Sep 13 10:00:57 2019 -0700
    get the warning message out of the warning only message to be used elsewhere and add measureTiming printout to hgGateway refs #23217
• src/hg/inc/hic.h
  • lines changed 6, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/inc/hicUi.h
  • lines changed 12, context: html, text, full: html, text
    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/lib/botDelay.c
  • lines changed 1, context: html, text, full: html, text
    832026164cc5f13b2764e5556bf003864d662938 Mon Sep 9 14:19:33 2019 -0700
    now allowing hgCustom to play the bottleneck game, and bold highlight the error 429 message refs #23217
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    cdae2fc61c0a4e03c2dee7321c91a42aa1ebdfc0 Mon Sep 9 15:43:17 2019 -0700
    now getting hgTables into the earlyBotCheck() game and fixup earlyBotCheck() to honor the exception list and default to a delay fraction value of 1.0 refs #23217
  • lines changed 1, context: html, text, full: html, text
    6c953808328fb7f034e4a36e99dc1ce326859508 Mon Sep 9 15:44:35 2019 -0700
    missing a ; line end character refs #23217
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    ca3f45c0d7c8ea372d9202eb5160c0f9268c95f2 Wed Sep 11 10:38:12 2019 -0700
    use the correct default delay fraction refs #23217
  • lines changed 58, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
  • lines changed 17, context: html, text, full: html, text
    74c99d39c800193f07a881ce98ee4b7065cee6dc Fri Sep 13 10:00:57 2019 -0700
    get the warning message out of the warning only message to be used elsewhere and add measureTiming printout to hgGateway refs #23217
• src/hg/lib/customTrack.c
  • lines changed 5, context: html, text, full: html, text
    a47f57d008f2db28a7b140ece87cbcfb8e8a5c0c Thu Sep 12 14:18:19 2019 -0700
    expand earlyBotCheck to manage two types of outputs, recognize defaults, and adding hgGateway to the game refs #23217
• src/hg/lib/hic.c
  • lines changed 9, context: html, text, full: html, text
    7c815153cdd9486e0edf61e9bffbeec1a5fb189e Wed Sep 11 16:04:23 2019 -0700
    A couple more files for the hic composite track changes, refs #22316
• src/hg/lib/hicUi.c
  • lines changed 118, context: html, text, full: html, text
    7c815153cdd9486e0edf61e9bffbeec1a5fb189e Wed Sep 11 16:04:23 2019 -0700
    A couple more files for the hic composite track changes, refs #22316
• src/hg/lib/hubConnect.c
  • lines changed 47, context: html, text, full: html, text
    658bb95a9b155d3f759744f760320e90e99fe2d8 Fri Sep 13 10:59:53 2019 -0700
    allow a comma-separated list in hubUrl statements
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    f2d99f0c3d73e67c3c89b318f61bcce0daae599b Sat Sep 14 10:25:14 2019 -0700
    look for multiple hubUrl on the URL rather than allowing commas in the setting.
• src/hg/lib/hui.c
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    590e91b4174d19f21ab58ba55ec25903298f8a3c Fri Sep 13 10:43:35 2019 -0700
    use "group auto-scale" for cumulative auto-scale
• src/hg/lib/straw/straw.cpp
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    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/lib/straw/straw.h
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    b2acdf83569bcb30013ed09d885d3f48b19c1d4e Wed Sep 11 16:03:26 2019 -0700
    Better support for hic composite tracks, and hic trackUi pages now include metadata from the file, refs #22316
• src/hg/lib/trackHub.c
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    375571ebe2624dcb95cf0907676f966f74108adb Tue Sep 10 09:52:06 2019 -0700
    allow track hubs to attack to an assembly hub
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    4702585f8f9e47c84018f5d7d5ff904ed8972358 Wed Sep 11 16:01:21 2019 -0700
    Adding hic to the list of allowed track types for hubs, refs #22316
• src/hg/makeDb/doc/regenRn0/initialBuild.txt
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    e932767ea60a610752038c2c42713e0fd48645a6 Wed Sep 11 10:23:49 2019 -0700
    build regenRn0 browser refs #21579
• src/hg/makeDb/doc/regenRn1/initialBuild.txt
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    75343bb8e3633b0b942731a7649c6b009c2bb769 Wed Sep 11 08:49:49 2019 -0700
    beginning next Rat refs #21579
• src/hg/makeDb/doc/rn6.txt
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    5002bc264773860c46470525d2f8802f2c45679a Wed Sep 11 09:37:10 2019 -0700
    liftOver to regenRn0 and regenRn1 refs #21579
• src/hg/makeDb/genbank/etc/align.dbs
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    c890de997de350a495d4c58118fba49159a1b297 Wed Sep 11 09:01:51 2019 -0700
    Added regenRn1 - Regeneron rat refs #21579
• src/hg/makeDb/genbank/etc/genbank.conf
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    711a43a7e71b5dc994106d21f9b3254fe48b009b Wed Sep 11 08:59:03 2019 -0700
    Added regenRn1 - Regeneron rat refs #21579
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    c890de997de350a495d4c58118fba49159a1b297 Wed Sep 11 09:01:51 2019 -0700
    Added regenRn1 - Regeneron rat refs #21579
• src/hg/makeDb/kgAllocId/kgAllocId.c
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    2670d57795b4b8ff02a480f97adcfdc0b3304a11 Mon Sep 9 13:59:07 2019 -0700
    add some comments in response to code review
• src/hg/makeDb/schema/all.joiner
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    68937bef9a85069b771cbdf25a782c9f62b9bcf6 Thu Sep 12 14:46:35 2019 -0700
    adding rules for regenRn1 refs #21579
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
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    a4c0e0fee26fceb3ed97a63e34044c2aa5a996e5 Wed Sep 11 14:36:55 2019 -0700
    Fixing species table on the cons124way description page, refs #24039
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra
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    feb3d230bcedf8f675a2e7fa3ff07201840ada55 Tue Sep 10 11:29:21 2019 -0700
    Changing gdc all cancer long label to be more accurate, refs #24026
• src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
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    fb30d552b09686ac1f7d26d10ea821c0e3a0f821 Wed Sep 11 14:56:49 2019 -0700
    Correct P0 long labels. refs #23970
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    5f8bd704e0605123dfdd32087d8fd70f74091676 Wed Sep 11 15:19:20 2019 -0700
    Minor label relabeling and file renaming. refs #23880
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    5b98413917254114a1219389ec8b9ee0668df170 Wed Sep 11 16:43:50 2019 -0700
    Tweak default on tracks. refs #23990
• src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
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    1b9178e6f9a4093b47848db5d037a704c7352749 Wed Sep 11 15:01:09 2019 -0700
    Correct P0 long labels. refs #24128
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    5f8bd704e0605123dfdd32087d8fd70f74091676 Wed Sep 11 15:19:20 2019 -0700
    Minor label relabeling and file renaming. refs #23880
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    a7926f9fedb679fc0a1fade0c4f21311d7f32dc6 Wed Sep 11 15:28:18 2019 -0700
    Trim shortlabels. refs #24128
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    5b98413917254114a1219389ec8b9ee0668df170 Wed Sep 11 16:43:50 2019 -0700
    Tweak default on tracks. refs #23990
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    af461ddaef211c16a3ca52913df3f4c9a95ed48d Thu Sep 12 13:38:55 2019 -0700
    Extend labelOnFeature setting to support dense mode w/o labels (as usual in our tracks). Using this feature in chromatin state tracks. refs #24128
• src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
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    da82c8df231e66625b605ff7dac241d47d3ee0dc Wed Sep 11 14:55:02 2019 -0700
    Replace offending dots in track names from Ren lab hub. refs #23693
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    5b98413917254114a1219389ec8b9ee0668df170 Wed Sep 11 16:43:50 2019 -0700
    Tweak default on tracks. refs #23990
• src/hg/makeDb/trackDb/mouse/mm10/encode3Reg.html
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
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    0ad9db5d262850c4b159bad0eb9831ddd1e97cbb Wed Sep 11 15:11:54 2019 -0700
    Fix link. refs #23880
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    70eb0c6ecc1ae9d8cc66c1bc59e477ac1eb91d9f Wed Sep 11 15:18:19 2019 -0700
    Add link. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenAtac.html
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    2876cdada90cb8d845ab0b06cec817f83346400a Thu Sep 12 13:59:17 2019 -0700
    Add color patches to track description. refs #23693
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    fe51985b7657e446612d290edc989d5861a4fa4e Fri Sep 13 09:33:52 2019 -0700
    Remove DOS line ends.
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenChromHmm.html
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    f6e23d1d07c38b1a7cefd03393ec92856d5bb71c Thu Sep 12 12:42:57 2019 -0700
    Polish track description. refs #24128
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    af461ddaef211c16a3ca52913df3f4c9a95ed48d Thu Sep 12 13:38:55 2019 -0700
    Extend labelOnFeature setting to support dense mode w/o labels (as usual in our tracks). Using this feature in chromatin state tracks. refs #24128
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.html
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    cd91480db30f283eddedba67051be27b6522ec15 Wed Sep 11 14:40:34 2019 -0700
    Refine long labels. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.ra
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    cd91480db30f283eddedba67051be27b6522ec15 Wed Sep 11 14:40:34 2019 -0700
    Refine long labels. refs #23693
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
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    36cb847f6b7291b1cb47fa503dbfd3c9beca741d Wed Sep 11 17:10:11 2019 -0700
    Fix up filename problem. refs #23881
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenHistone.html
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    2876cdada90cb8d845ab0b06cec817f83346400a Thu Sep 12 13:59:17 2019 -0700
    Add color patches to track description. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/enhancerGeneInteract.html
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    172d7a0e89e4ad6b243adad0fc6c5b97abd93052 Tue Aug 6 16:28:07 2019 -0700
    Add track description. refs #23881
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    cd91480db30f283eddedba67051be27b6522ec15 Wed Sep 11 14:40:34 2019 -0700
    Refine long labels. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.atac.ra
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    0704d60df5fb8dca2aacab2a553477397bb26af1 Wed Aug 7 16:42:47 2019 -0700
    Add ATAC-seq track, tune up track config for related tracks. refs #23970
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    8d264f60e756c0949a00e443988305e45ea1d695 Mon Sep 9 15:19:41 2019 -0700
    Use pooled bed files (update from Ren lab). refs #23970
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    52415ddd22b076a8da4d20f36fa5bd417eec9a92 Mon Sep 9 15:24:45 2019 -0700
    Remove superfluous lines. refs #23880
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    d13cfad020fadc5a52eaa649b048308f593da89e Mon Sep 9 15:28:04 2019 -0700
    Cleanup. refs #23880
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.chromHmm.ra
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    0704d60df5fb8dca2aacab2a553477397bb26af1 Wed Aug 7 16:42:47 2019 -0700
    Add ATAC-seq track, tune up track config for related tracks. refs #23970
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
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    c1e0d2307cfe3e7c75cfd54ae8626a797d5b7adb Sun Jul 28 20:20:04 2019 -0700
    Enhancer/gene interact track. refs #23881
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    75f11715852d9fc54c7f0eb6b7a12665d913fd7e Wed Jul 31 16:43:00 2019 -0700
    Track config for mouse enhancer/gene track from Ren lab + EPDNew. refs #23881
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    0704d60df5fb8dca2aacab2a553477397bb26af1 Wed Aug 7 16:42:47 2019 -0700
    Add ATAC-seq track, tune up track config for related tracks. refs #23970
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
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    ecdc82eb342c99c36ac63c963cd2261003595a0f Wed Sep 11 16:44:37 2019 -0700
    Tweak default on tracks. refs #23990
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.enhancerGeneInteract.ra
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    75f11715852d9fc54c7f0eb6b7a12665d913fd7e Wed Jul 31 16:43:00 2019 -0700
    Track config for mouse enhancer/gene track from Ren lab + EPDNew. refs #23881
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    52f070230fc74d3e6b45fc5ac13d4a8b051d7b0a Tue Aug 6 15:48:19 2019 -0700
    Expand to two datasets (all and replicated), following pattern of GeneHancer. refs #23881
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    0704d60df5fb8dca2aacab2a553477397bb26af1 Wed Aug 7 16:42:47 2019 -0700
    Add ATAC-seq track, tune up track config for related tracks. refs #23970
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    280b6ce6b208cdb9a6c78f22de7eca58ac9d7710 Wed Sep 11 10:27:22 2019 -0700
    Clarification on long labels. refs #23693
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    cd91480db30f283eddedba67051be27b6522ec15 Wed Sep 11 14:40:34 2019 -0700
    Refine long labels. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra
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    0704d60df5fb8dca2aacab2a553477397bb26af1 Wed Aug 7 16:42:47 2019 -0700
    Add ATAC-seq track, tune up track config for related tracks. refs #23970
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    b48c2ab7665ace5fbbb62dd8496a759f7533bf02 Mon Aug 12 09:10:09 2019 -0700
    Swap short label orders to match other tracks. refs #23693
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    280b6ce6b208cdb9a6c78f22de7eca58ac9d7710 Wed Sep 11 10:27:22 2019 -0700
    Clarification on long labels. refs #23693
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    cd91480db30f283eddedba67051be27b6522ec15 Wed Sep 11 14:40:34 2019 -0700
    Refine long labels. refs #23693
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    5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700
    Cleanup ra files, add html. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    75f11715852d9fc54c7f0eb6b7a12665d913fd7e Wed Jul 31 16:43:00 2019 -0700
    Track config for mouse enhancer/gene track from Ren lab + EPDNew. refs #23881
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    5f8bd704e0605123dfdd32087d8fd70f74091676 Wed Sep 11 15:19:20 2019 -0700
    Minor label relabeling and file renaming. refs #23880
• src/hg/pyLib/hgLib.py
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    d4357f00f0592923ed6376bdf489072c3cb1e0af Mon Sep 9 12:14:08 2019 -0700
    fixing small problem in last comment, code review, refs #24108
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    69053e55a7502bb79acb350f002a277ce330cad9 Tue Sep 10 03:26:43 2019 -0700
    adding the retry-after header to hgLib's bottleneck when blocking, pending Jonathan's/Hiram's feedback, refs #24094
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    e940236873e8a6fe882adec2465f0aa45417db81 Wed Sep 11 04:14:09 2019 -0700
    adding cookie bottleneck logic to hgGeneGraph, refs #24094
• src/hg/sqlUpdateRelated/sqlUpdateRelated.c
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    3e6c9b3323a9875d9163e6f4fc28c35c92717985 Fri Sep 6 14:07:07 2019 -0700
    Making it optionally tolerate missing files in the command line without complaint.
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    285594d7319101feb853a740494f511e37c5c180 Sat Sep 14 14:25:49 2019 -0700
    Adding an update option which parallels the conditional option in some ways.
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    6f32b1ba12ffa50bdffefd5cc88ea12141f1334a Sat Sep 14 14:33:04 2019 -0700
    Started to document how fields work in usage message. Not complete. My, this code could use a couple of functions broken up too - logic is a little tortured and long now. Alas it's gonna be the sort of refactor where the functions are going to have 8 parameters each if I break up the big one.
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    0890e2c3c68649027aa95195fe82ca2e1101e82e Sun Sep 15 11:42:11 2019 -0700
    Adding -uncsv as an option. Actually it used to be the default so I had to throw it on in the test set. The csv/array vs. normal commas in free text are a weak point of the system. Between that and the SQL you can't escape escaping it seems!
• src/hg/sqlUpdateRelated/tests/doTest.csh
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    0890e2c3c68649027aa95195fe82ca2e1101e82e Sun Sep 15 11:42:11 2019 -0700
    Adding -uncsv as an option. Actually it used to be the default so I had to throw it on in the test set. The csv/array vs. normal commas in free text are a weak point of the system. Between that and the SQL you can't escape escaping it seems!
• src/hg/utils/phyloTrees/commonNames.sh
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    0dcda7d7e41d042cdc893034b076b9e70d489af0 Wed Sep 11 12:15:48 2019 -0700
    fix incorrect name for apaVit1 refs #22687
• src/inc/strex.h
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    b115bef91d8de7132ccdbeca330a9941a5ffee65 Thu Sep 5 16:27:05 2019 -0700
    Fixed a few typos in comments and docs.
• src/lib/strex.c
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    45339e6f4ac8777701d3ecad108d8eee2b942ed8 Thu Sep 5 16:33:00 2019 -0700
    Updating docs which had drifted a little from implementation, in the comments.
• src/lib/strex.doc
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    b115bef91d8de7132ccdbeca330a9941a5ffee65 Thu Sep 5 16:27:05 2019 -0700
    Fixed a few typos in comments and docs.
• src/tabFile/tabToTabDir/tabToTabDir.c
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    c4c03a112fa516468b6ce875108c5b1749e11104 Fri Sep 6 14:08:20 2019 -0700
    Making it so that a newField can have a ? before it, in which case if the corresponding oldField is missing it is not an error, it simply is skipped.
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    0b7fc0972a745005ac329190569f51b12877ebe0 Sun Sep 15 15:24:53 2019 -0700
    Adding unroll for unpacking csv arrays into a table with multiple rows. The driving use case is the contacts/contributors merge for HCA.
• src/tabFile/tabToTabDir/tests/expected/unroll_test.tsv
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    0b7fc0972a745005ac329190569f51b12877ebe0 Sun Sep 15 15:24:53 2019 -0700
    Adding unroll for unpacking csv arrays into a table with multiple rows. The driving use case is the contacts/contributors merge for HCA.
• src/tabFile/tabToTabDir/tests/input/spec.txt
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    0b7fc0972a745005ac329190569f51b12877ebe0 Sun Sep 15 15:24:53 2019 -0700
    Adding unroll for unpacking csv arrays into a table with multiple rows. The driving use case is the contacts/contributors merge for HCA.
• src/utils/qa/weeklybld/buildEnv.csh
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    3ca7d5b6df63fa6cfbc0800b5b2051512868453d Mon Sep 16 10:12:35 2019 -0700
    v388 preview2, refs #24138

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