All File Changes

v334_base to v335_preview (2016-06-13 to 2016-06-20) v335

• confs/hgwbeta.hg.conf
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    59ddc220eaa8f5c0f8e5dd1aa6ec27e671d3b520 Sun Jun 19 01:11:40 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwCheckDataset/cdwCheckDataset.c
  • lines changed 1, context: html, text, full: html, text
    c4eb0dae6360ea6f9b9c222f0fbcf64a4c68d262 Mon Jun 20 09:58:07 2016 -0700
    Removing unused variables, refs #17187
    
• src/hg/cirm/cdw/cdwCheckValidation/cdwCheckValidation.c
  • lines changed 10, context: html, text, full: html, text
    448276e67886b89b4fbaac3c79983e1846d5f794 Mon Jun 20 09:57:08 2016 -0700
    Fixing a bug that was casting a string to int directly, refs #17100
    
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 3, context: html, text, full: html, text
    e44b0a045aede042d49b720e6d964eb47119a722 Thu Jun 16 09:55:48 2016 -0700
    Escaping value strings as they go into the cdwFileTags table.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwFlowCharts.c
  • lines changed 346, context: html, text, full: html, text
    c703b5a7af01f347733a4755ab22733b2e5a319a Thu Jun 16 15:18:09 2016 -0700
    Cleaning things up a bit, moving the file into a local module refs #17544
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwFlowCharts.h
  • lines changed 45, context: html, text, full: html, text
    c703b5a7af01f347733a4755ab22733b2e5a319a Thu Jun 16 15:18:09 2016 -0700
    Cleaning things up a bit, moving the file into a local module refs #17544
    
  • lines changed 42, context: html, text, full: html, text
    a4beb676d90bddca1c2a095f23a45a6c930a1e1d Thu Jun 16 15:22:50 2016 -0700
    Removing code cruft refs #17544
    
• src/hg/cirm/cdw/flowCharts/sqlToTxt/sqlToTxt.c
  • lines changed 392, context: html, text, full: html, text
    c56565c02c07147222978802a02205b69256ae1f Tue Jun 14 11:12:42 2016 -0700
    Moved the program sqlToTxt into this library file cdwFlowCharts, this library supports file flowcharts, refs #16113
    
• src/hg/cirm/cdw/inc/cdwFlowCharts.h
  • lines changed 45, context: html, text, full: html, text
    09a75a128b6e810bfcf4955d0f75fdb599d95292 Wed Jun 15 15:18:22 2016 -0700
    Adding in the header file, refs #17544
    
  • lines changed 45, context: html, text, full: html, text
    c703b5a7af01f347733a4755ab22733b2e5a319a Thu Jun 16 15:18:09 2016 -0700
    Cleaning things up a bit, moving the file into a local module refs #17544
    
• src/hg/cirm/cdw/lib/cdwFlowCharts.c
  • lines changed 325, context: html, text, full: html, text
    c56565c02c07147222978802a02205b69256ae1f Tue Jun 14 11:12:42 2016 -0700
    Moved the program sqlToTxt into this library file cdwFlowCharts, this library supports file flowcharts, refs #16113
    
  • lines changed 16, context: html, text, full: html, text
    4bf63ab386b34f9e23972f4dd152021ee8814725 Tue Jun 14 11:26:59 2016 -0700
    fixing up a bug that was causing the table to not be displayed on certain files, refs #16113
    
  • lines changed 339, context: html, text, full: html, text
    c703b5a7af01f347733a4755ab22733b2e5a319a Thu Jun 16 15:18:09 2016 -0700
    Cleaning things up a bit, moving the file into a local module refs #17544
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 4, context: html, text, full: html, text
    c56565c02c07147222978802a02205b69256ae1f Tue Jun 14 11:12:42 2016 -0700
    Moved the program sqlToTxt into this library file cdwFlowCharts, this library supports file flowcharts, refs #16113
    
• src/hg/geoIp/README
  • lines changed 65, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
  • lines changed 2, context: html, text, full: html, text
    adfd7617b6dad6537fd1fbab1b5f44710fabdf64 Mon Jun 13 16:43:56 2016 -0700
    oops, need newer version of geoIpToCountry.c because we do NOT want dotted-quad format. Simple integers are fast and work well in the database.
    
  • lines changed 191, context: html, text, full: html, text
    04b288b4920e8aea8f97f029a4c08c3f2499673b Tue Jun 14 14:24:06 2016 -0700
    Adding detailed HOWTO notes for geoIp update process.
    
  • lines changed 1, context: html, text, full: html, text
    269421056006b2060ce04dca9660fcbe8f5798af Fri Jun 17 11:42:32 2016 -0700
    updated gbNode.shortLabel for node 3.
    
• src/hg/geoIp/README_OLD
  • lines changed 67, context: html, text, full: html, text
    04b288b4920e8aea8f97f029a4c08c3f2499673b Tue Jun 14 14:24:06 2016 -0700
    Adding detailed HOWTO notes for geoIp update process.
    
• src/hg/geoIp/continent.as
  • lines changed 7, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/continentToNode.as
  • lines changed 7, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/country.as
  • lines changed 7, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/countryToContinent.as
  • lines changed 7, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/countryToNode.as
  • lines changed 6, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/gbNode.as
  • lines changed 9, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/geoIpCountry.as
  • lines changed 8, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/geoIpNode.as
  • lines changed 8, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/geoIpToCountry.c
  • lines changed 93, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
  • lines changed 18, context: html, text, full: html, text
    adfd7617b6dad6537fd1fbab1b5f44710fabdf64 Mon Jun 13 16:43:56 2016 -0700
    oops, need newer version of geoIpToCountry.c because we do NOT want dotted-quad format. Simple integers are fast and work well in the database.
    
• src/hg/geoIp/load-tables
  • lines changed 11, context: html, text, full: html, text
    8554403a3f057a38f35d763783f95ee64b247b80 Tue Jun 14 12:32:30 2016 -0700
    adding a way to run these
    
• src/hg/geoIp/make-sql
  • lines changed 10, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/geoIp/makefile
  • lines changed 21, context: html, text, full: html, text
    a0f005d70ecb78a51580a8247a1755f9c53e74d2 Mon Jun 13 16:23:42 2016 -0700
    Initial check-in of geoIp basics.
    
• src/hg/hgSession/hgSession.c
  • lines changed 5, context: html, text, full: html, text
    5d33200cf63bcca9561ac00456bd7ec040b9b616 Tue Jun 14 00:30:19 2016 -0700
    Fix for cart improperly deleting table state variables, refs #17519
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 15, context: html, text, full: html, text
    f2e106b897f58f772d3a25713bb3ede142ae4bd5 Mon Jun 13 15:58:12 2016 -0700
    add next/prev item navigation to longTabix support
    
  • lines changed 1, context: html, text, full: html, text
    6fb15efe4ba9f2618b662d97c510f2d3a8c14c28 Tue Jun 14 11:19:55 2016 -0700
    Fix query with hard-coded location for refLink #17528
    
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 6, context: html, text, full: html, text
    12265fa6113a17937be914d7ae7406cff4fcc773 Wed Jun 15 16:31:32 2016 -0700
    First edits on bigStar.html files, refs #17325
    
  • lines changed 72, context: html, text, full: html, text
    d4e255845d9cbeef660c4c9e5018d27d6577e02e Fri Jun 17 08:27:15 2016 -0700
    Mostly tag and spacing fixes on bigChain doc, refs #17325
    
  • lines changed 92, context: html, text, full: html, text
    f435f8fa8cf61dab9f1abb301181bea014a15ac6 Fri Jun 17 15:53:45 2016 -0700
    More fixups to bigPsl doc, started on restructuring and edits to bigChain doc. Incoporated all of Braney's makedoc info into bigChain doc as well. refs #17325
    
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 6, context: html, text, full: html, text
    12265fa6113a17937be914d7ae7406cff4fcc773 Wed Jun 15 16:31:32 2016 -0700
    First edits on bigStar.html files, refs #17325
    
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 5, context: html, text, full: html, text
    12265fa6113a17937be914d7ae7406cff4fcc773 Wed Jun 15 16:31:32 2016 -0700
    First edits on bigStar.html files, refs #17325
    
  • lines changed 126, context: html, text, full: html, text
    9d8c663841ea3d86c469ee3e6a7a7e0daabda994 Thu Jun 16 16:46:23 2016 -0700
    Fixup of bigPsl doc. Mostly tag cleanup due to inconsistent formatting, and some restructuring. Incorporated Braney's makedoc steps as well. Still needs a little more cleanup, refs #17325
    
  • lines changed 27, context: html, text, full: html, text
    f435f8fa8cf61dab9f1abb301181bea014a15ac6 Fri Jun 17 15:53:45 2016 -0700
    More fixups to bigPsl doc, started on restructuring and edits to bigChain doc. Incoporated all of Braney's makedoc info into bigChain doc as well. refs #17325
    
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 42, context: html, text, full: html, text
    b64fe133dcdc3861b0689843905b88dd95ad7137 Mon Jun 13 15:34:50 2016 -0700
    updated mirror doc, added genome-asia info
    
  • lines changed 3, context: html, text, full: html, text
    97793eec75dbad1c7e3402ef8f3951d13117e5e5 Wed Jun 15 14:45:41 2016 -0700
    added link to riken campus
    
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    df1b4bbb3060284b0f94c0006cd33311341bbbf4 Wed Jun 15 14:49:23 2016 -0700
    fixed forgeign letter and spelling mistake
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 1, context: html, text, full: html, text
    db2089c84f664a81d809d22bab2914192a67def0 Wed Jun 15 10:08:06 2016 -0700
    two tiny readability tweaks to unrelated files
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 1, context: html, text, full: html, text
    a1d0235b1f56727ece4f7e9f3ae2c34ef26d6641 Thu Jun 9 16:22:37 2016 -0700
    fixed a wrong word, per Matt. refs #17483
    
  • lines changed 1, context: html, text, full: html, text
    db2089c84f664a81d809d22bab2914192a67def0 Wed Jun 15 10:08:06 2016 -0700
    two tiny readability tweaks to unrelated files
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    92a0ea9f36380d35645f891c2dee6ca5ae823ce3 Tue Jun 14 14:36:52 2016 -0700
    Removing hard-coded link to kuhn sandbox, no redmine
    
  • lines changed 45, context: html, text, full: html, text
    666bdbc36cb0424e926fb7f68da05fe5be3aad8d Wed Jun 15 14:40:05 2016 -0700
    added genome-asia announcement to archives
    
• src/hg/htdocs/images/Colobus_angolensis_palliatus.jpg
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    007750fdc6a41738f4ea6b139553c62d6a9ecdee Wed Jun 15 09:44:47 2016 -0700
    photo from Eric Kilby https://www.flickr.com/people/8749778@N06 refs #17545
    
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    92a0ea9f36380d35645f891c2dee6ca5ae823ce3 Tue Jun 14 14:36:52 2016 -0700
    Removing hard-coded link to kuhn sandbox, no redmine
    
  • lines changed 88, context: html, text, full: html, text
    44b656609fe0b77c1162f052d94217bc04ccb916 Wed Jun 15 14:26:32 2016 -0700
    added news announcement for genome-mirror
    
  • lines changed 1, context: html, text, full: html, text
    d02ee7d544b482f50228404602166c46520b697a Wed Jun 15 14:31:33 2016 -0700
    fixed a mistake in news announcement
    
• src/hg/inc/sessionThumbnail.h
  • lines changed 7, context: html, text, full: html, text
    156c6fa583c7a87e731d927b42ca86d772e06e77 Wed Jun 15 11:32:10 2016 -0700
    Changes to place session thumbnails in trash/hgPS, refs #15312
    
• src/hg/lib/chromGraphFactory.c
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    ccea6bc0ed00118adc05466c7b22531c8d172ad4 Thu Jun 16 18:48:10 2016 -0700
    fixes #16983. Huge 150 million row snp table was not able to be loaded into a hash. Now for snp tables, it just looks up the individual markers with a quick query on the name index. Can handle more than 500,000 markers without timing out.
    
• src/hg/lib/gtexGeneBed.as
  • lines changed 3, context: html, text, full: html, text
    fcdc06a5a7ad71e42226eff44a00d772c7338d21 Wed Jun 15 11:48:35 2016 -0700
    Additional description of GTEx schema score fields and how they are used in display. Prompted by inquiry of Jeff Streuwing (NIH program director for GTEx).
    
• src/hg/lib/sessionThumbnail.c
  • lines changed 35, context: html, text, full: html, text
    156c6fa583c7a87e731d927b42ca86d772e06e77 Wed Jun 15 11:32:10 2016 -0700
    Changes to place session thumbnails in trash/hgPS, refs #15312
    
• src/hg/makeDb/doc/colAng1/initialBuild.txt
  • lines changed 654, context: html, text, full: html, text
    d4ccc19e4a6948ff4f7300c6d28b42955b1779b7 Fri Jun 17 16:47:41 2016 -0700
    masking done ready for genbank refs #17545
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
  • lines changed 12, context: html, text, full: html, text
    011f520dc7b5ed3e52e2c556340a28e2f84cee28 Fri Jun 17 17:33:36 2016 -0700
    make Pfam track pay attention to the minimum significant score values.
    This removes the noise from this track.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    c292a536a9d3e92418fb98e458f5322e9234f2b1 Fri Jun 17 15:20:09 2016 -0700
    add hg38Patch7 definitions refs #17134
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 3, context: html, text, full: html, text
    fcdc06a5a7ad71e42226eff44a00d772c7338d21 Wed Jun 15 11:48:35 2016 -0700
    Additional description of GTEx schema score fields and how they are used in display. Prompted by inquiry of Jeff Streuwing (NIH program director for GTEx).
    
  • lines changed 5, context: html, text, full: html, text
    161b323952cf54781f76eb447c6695c424f07f42 Wed Jun 15 11:52:52 2016 -0700
    Tidy up.
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch7.html
  • lines changed 391, context: html, text, full: html, text
    613865900bf13d1d44cb42d17b7606bc242b1b38 Fri Jun 17 15:21:24 2016 -0700
    description page for patch 7 refs #17134
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    932477786eed5310e831e6f7832e35ce4984884d Wed Jun 15 14:05:37 2016 -0700
    reenable 145way conservation track refs #17286
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    482567637e6ef3f00468b78b2c07238ebdb5d4d7 Mon Jun 13 16:44:28 2016 -0700
    Adjusting release tag for no-genome OMIM tracks on beta, refs #4458
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    bc7876d2e6471be489ccc7e0f3ecf33c5ca52eaf Wed Jun 15 11:09:36 2016 -0700
    adding colAng1 to the build refs #17545
    
• src/hg/makeDb/trackDb/mouse/mm10/knownGeneOld8.html
  • lines changed 1, context: html, text, full: html, text
    392feffcc8be479c821beb5e4ae35660485fedab Mon Jun 13 11:31:37 2016 -0700
    Fixing typo of knownGene count on desc page, refs #15315
    
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/description.html
  • lines changed 64, context: html, text, full: html, text
    bc7876d2e6471be489ccc7e0f3ecf33c5ca52eaf Wed Jun 15 11:09:36 2016 -0700
    adding colAng1 to the build refs #17545
    
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/gap.html
  • lines changed 30, context: html, text, full: html, text
    bc7876d2e6471be489ccc7e0f3ecf33c5ca52eaf Wed Jun 15 11:09:36 2016 -0700
    adding colAng1 to the build refs #17545
    
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/gold.html
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    bc7876d2e6471be489ccc7e0f3ecf33c5ca52eaf Wed Jun 15 11:09:36 2016 -0700
    adding colAng1 to the build refs #17545
    
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.ra
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    bc7876d2e6471be489ccc7e0f3ecf33c5ca52eaf Wed Jun 15 11:09:36 2016 -0700
    adding colAng1 to the build refs #17545
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fff275ac504ad3b346a7f23b7f8ad8014e36cf3a Wed Jun 15 09:20:19 2016 -0700
    Adding beta release tag to oreganno track, refs #17278
    
• src/hg/oneShot/freen/freen.c
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    73898faded5e965fe61ceee6773709d3ab3cd3e5 Wed Jun 8 15:51:48 2016 -0700
    Prototyping a function to figure out cdw database name for sandboxes.
    
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 5, context: html, text, full: html, text
    38a1ce0e1e851687f672c40fdd1ec807e66d89d9 Tue Jun 14 15:56:55 2016 -0700
    fixing a makeTableList problem reported by Jorge
    
• src/hg/utils/otto/decipher/login.perl
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    0662e76ea058afebc9c1400b5ca98f05baf01bdc Mon Jun 13 16:13:31 2016 -0700
    Fix for Decipher track otto-loader - script should now download the correct file
    
• src/inc/bedTabix.h
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    f2e106b897f58f772d3a25713bb3ede142ae4bd5 Mon Jun 13 15:58:12 2016 -0700
    add next/prev item navigation to longTabix support
    
• src/inc/portable.h
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    156c6fa583c7a87e731d927b42ca86d772e06e77 Wed Jun 15 11:32:10 2016 -0700
    Changes to place session thumbnails in trash/hgPS, refs #15312
    
• src/lib/bedTabix.c
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    f2e106b897f58f772d3a25713bb3ede142ae4bd5 Mon Jun 13 15:58:12 2016 -0700
    add next/prev item navigation to longTabix support
    
• src/product/README.cram
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    6ee25f2ac4498907104ca42df870b444f5d8a4a3 Mon Jun 13 15:52:04 2016 -0700
    README that describes how to set up CRAM support in the browser, refs #14717
    
• src/product/ex.hg.conf
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    dbe284a55009a75648c02e56891b89b3ca92f8e3 Wed Jun 15 09:29:57 2016 -0700
    Adding example hg.conf entry for CRAM reference fetch, refs #14717
    
• src/product/installer/README.md
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    9be24197995cf860740e1c399a0efcd8e72ad088 Mon Jun 13 16:44:25 2016 -0700
    Minor edits to gbic help doc, refs #14399
    
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    a569d948ffe23dc302174579c6a1c6c13f29eafb Tue Jun 14 11:47:46 2016 -0700
    More fixup of GBiB user guide. Replaced reference to github account with link to genome-store, refs #14399
    
• src/product/installer/browserSetup.sh
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    87853cac8cc1f853a031ab34366a18a73e8e4ae3 Tue Jun 14 11:43:26 2016 -0700
    Fixing typo in help message, refs #14399
    
• src/utils/qa/weeklybld/buildEnv.csh
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    3d7ff5b729639e4c510fefe2ebc323046e2ef78f Mon Jun 20 10:19:04 2016 -0700
    v335 preview1 refs #17457
    
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    b5f2ebc729a28718f7a8b4c78e86a5bc59de65f6 Wed Jun 15 11:59:46 2016 -0700
    Changing build robot script to use hg38 instead of hg19.
    

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• files changed: 86