All File Changes

v379_preview2 to v379_base (2019-03-11 to 2019-03-18) v379

• confs/hgwbeta.hg.conf
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    6c218c3e7d559330dcc605c6a172931d976b5be5 Sun Mar 17 01:11:43 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
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    5cb623953a65af10be7cfeab7c56615cbf9fc147 Thu Mar 14 13:13:46 2019 -0700
    Changes based on code review. Fixing a bunch of stuff broken when changing FontAwesome versions. Minor wording corrections. refs #23100
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
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    5cb623953a65af10be7cfeab7c56615cbf9fc147 Thu Mar 14 13:13:46 2019 -0700
    Changes based on code review. Fixing a bunch of stuff broken when changing FontAwesome versions. Minor wording corrections. refs #23100
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 14, context: html, text, full: html, text
    5cb623953a65af10be7cfeab7c56615cbf9fc147 Thu Mar 14 13:13:46 2019 -0700
    Changes based on code review. Fixing a bunch of stuff broken when changing FontAwesome versions. Minor wording corrections. refs #23100
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 10, context: html, text, full: html, text
    5cb623953a65af10be7cfeab7c56615cbf9fc147 Thu Mar 14 13:13:46 2019 -0700
    Changes based on code review. Fixing a bunch of stuff broken when changing FontAwesome versions. Minor wording corrections. refs #23100
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 248, context: html, text, full: html, text
    5cb623953a65af10be7cfeab7c56615cbf9fc147 Thu Mar 14 13:13:46 2019 -0700
    Changes based on code review. Fixing a bunch of stuff broken when changing FontAwesome versions. Minor wording corrections. refs #23100
• src/hg/cirm/gateway/htdocs/tools.html
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    5cb623953a65af10be7cfeab7c56615cbf9fc147 Thu Mar 14 13:13:46 2019 -0700
    Changes based on code review. Fixing a bunch of stuff broken when changing FontAwesome versions. Minor wording corrections. refs #23100
• src/hg/hgGene/hgGeneData/Human/links.ra
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    76a1bbbc58274f3054742d4f0ea94953ab953f2f Wed Mar 13 09:21:52 2019 -0700
    Editing bad link for AllenBrain on Human, refs #23069
• src/hg/hgTracks/hgTracks.c
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    27612a60c0f8c1aefbe6ca7afcdf0c2deb73b98f Fri Mar 15 13:29:04 2019 -0700
    Missing NULL check -- caused SEGV for next/prev item of custom tracks, for which hTrackDb() returns NULL. (hgwdev-only, introduced Feb. 28th)
• src/hg/hgc/gencodeClick.c
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    6a723bb9ed92b58efb829e1c2dd5685d3d5329d0 Mon Mar 18 10:15:41 2019 -0700
    fix gencode hgc link to HGNC. Fixes #23133
• src/hg/hgc/hgc.c
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    ce84dec02479202e3c5da08720403faa4cf4f215 Thu Mar 14 12:09:42 2019 -0700
    support bigGenePred with no table as a native track
• src/hg/htdocs/FAQ/FAQgenes.html
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    120b2f4f3184b97ab54fe7c0d73c1bff97280599 Wed Mar 13 08:51:29 2019 -0700
    Small typo corrections to unreleased FAQgenes page ref#22696
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    a9767c7e8c280c556a08646f3a389d3cf7f75b16 Wed Mar 13 12:56:58 2019 -0700
    Corrections to unreleased FAQgenes page ref#22696
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    0f743323b9da96414336d5129e51e3e1e4a23287 Thu Mar 14 13:04:40 2019 -0700
    Working on unreleased FAQgenes page ref#22696
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    be1a99d19b7da33ede69e4a92207cff1613e4bb5 Thu Mar 14 13:44:56 2019 -0700
    Working on unreleased FAQgenes page ref#22696
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    31fcbdd89fc12e37ab6e9e05ebfa183f5e720021 Thu Mar 14 17:04:51 2019 -0700
    Working on unreleased genesFAQ page ref#22696
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    b40165f963c2080a8a34cdb4c3e39c64a117ee28 Fri Mar 15 10:05:56 2019 -0700
    made a few tweaks to Max's CCDS FAQ (thanks Max\!)
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    65d56546d60ce474e45761ab4873176c281cc5f5 Fri Mar 15 10:35:03 2019 -0700
    More work on unreleased genes FAQ ref#22696
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    d491d2940f237f16a01e3a5cd770487cb3dc27b5 Fri Mar 15 10:40:04 2019 -0700
    More work on unreleased genes FAQ ref#22696
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    1e04a1eb63b24edd26c5699e53906c9a8136b6e2 Fri Mar 15 10:41:23 2019 -0700
    I need to make alpha more... unreleased FAQgenes ref#22696
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    d92b94ede1ef1b52b5c53498a494633e6904fdb4 Fri Mar 15 13:31:52 2019 -0700
    More updates to unreleased FAQGenes page ref#22696
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    22520c016786e1f3772d47752de3dc7adb011faf Fri Mar 15 16:01:13 2019 -0700
    Working on unreleased FAQGenes page ref#22696
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 52, context: html, text, full: html, text
    3169e7be9b7d002e894fdcadd4b179af54545073 Wed Mar 13 11:43:31 2019 -0700
    Adding images and proofreading page #21582
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    df3c3771451f7b9c205a9adf31c5bc1e138a3b14 Wed Mar 13 11:45:50 2019 -0700
    Minor image modification #21582
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    bff474f6064002d41108e5222d11c51c55098d2c Wed Mar 13 12:04:10 2019 -0700
    Completing image addition #21283
• src/hg/htdocs/goldenPath/help/customTrackText.html
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    055197d6c5018ca06cf635eeeb2c2cef80f7afb2 Mon Mar 11 15:02:31 2019 -0700
    Editing formating on customTracktext.html, refs #23108
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    367156806c6028898c51418b61e297b590f399f9 Fri Mar 15 10:10:11 2019 -0700
    Adding a link to the wikipage about distributed storage providers in the #hosting section of TrackHubHelp refs #20224
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
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    4c4e7cce9a73f9a2112ac8354cd17e832ce5c85c Mon Mar 11 15:48:34 2019 -0700
    Fixing minor sentence confusion. Correcting example number #23107
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 1, context: html, text, full: html, text
    4c4e7cce9a73f9a2112ac8354cd17e832ce5c85c Mon Mar 11 15:48:34 2019 -0700
    Fixing minor sentence confusion. Correcting example number #23107
• src/hg/htdocs/goldenPath/newsarch.html
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    79f590251e66beae0bdf5e868cbbef8a6d36fdf3 Mon Mar 11 14:36:11 2019 -0700
    Changes to announcement for patchwork #18855
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 28, context: html, text, full: html, text
    8a26d223e032303df50a8e161b26c73ceb9c11ef Mon Mar 11 13:06:50 2019 -0700
    Adding more publications to pubs.html
  • lines changed 11, context: html, text, full: html, text
    a3776a1cebc8532e971dd137c7b4a91fc652c20c Fri Mar 15 14:34:40 2019 -0700
    Adding a publication to the pubs page.
  • lines changed 9, context: html, text, full: html, text
    1371c93fdfbc1912a1a5339f2946bef2c5851d7c Fri Mar 15 15:01:52 2019 -0700
    More pubs by Max for pubs.html
• src/hg/htdocs/images/codonColoring.png
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    3169e7be9b7d002e894fdcadd4b179af54545073 Wed Mar 13 11:43:31 2019 -0700
    Adding images and proofreading page #21582
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    bff474f6064002d41108e5222d11c51c55098d2c Wed Mar 13 12:04:10 2019 -0700
    Completing image addition #21283
• src/hg/htdocs/training/index.html
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    7e9762c5ea917a07a5f355b1ba0939c015a1631d Tue Mar 12 13:13:15 2019 -0700
    dropping austria and greece. moving puerto rico and madison to near upcoming list. adding ASHG to long-term
• src/hg/hubApi/apiUtils.c
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    aa487ff67c04e2961d0ff4b5ba1d4568fa1d6f17 Fri Mar 15 15:51:40 2019 -0700
    now using source tree version tag and alpha install rule to cgi-bin-api and cleaned up html errors refs #18869
• src/hg/hubApi/dataApi.h
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    aa487ff67c04e2961d0ff4b5ba1d4568fa1d6f17 Fri Mar 15 15:51:40 2019 -0700
    now using source tree version tag and alpha install rule to cgi-bin-api and cleaned up html errors refs #18869
• src/hg/hubApi/getData.c
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    aa487ff67c04e2961d0ff4b5ba1d4568fa1d6f17 Fri Mar 15 15:51:40 2019 -0700
    now using source tree version tag and alpha install rule to cgi-bin-api and cleaned up html errors refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 92, context: html, text, full: html, text
    aa487ff67c04e2961d0ff4b5ba1d4568fa1d6f17 Fri Mar 15 15:51:40 2019 -0700
    now using source tree version tag and alpha install rule to cgi-bin-api and cleaned up html errors refs #18869
  • lines changed 77, context: html, text, full: html, text
    185686eee12878de494bd96ab0e3e8be4c8d03ed Fri Mar 15 17:16:37 2019 -0700
    adding user documentation refs #18869
• src/hg/hubApi/makefile
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    aa487ff67c04e2961d0ff4b5ba1d4568fa1d6f17 Fri Mar 15 15:51:40 2019 -0700
    now using source tree version tag and alpha install rule to cgi-bin-api and cleaned up html errors refs #18869
• src/hg/inc/hgSeq.h
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    ce84dec02479202e3c5da08720403faa4cf4f215 Thu Mar 14 12:09:42 2019 -0700
    support bigGenePred with no table as a native track
• src/hg/inc/versionInfo.h
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    1480ab5517f7db63adba53747f687c4a73e69729 Mon Mar 18 10:22:57 2019 -0700
    New version number v379
• src/hg/lib/hgSeq.c
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    ce84dec02479202e3c5da08720403faa4cf4f215 Thu Mar 14 12:09:42 2019 -0700
    support bigGenePred with no table as a native track
• src/hg/lib/mane.as
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    a9bfddd1f195f8ca2c2cccad324c07a602804270 Wed Mar 13 15:31:37 2019 -0700
    add MANE track
• src/hg/lib/scopDesc.as
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    95575eb62326537cb3320ffe2857426cffa8241a Tue Mar 12 16:32:00 2019 -0700
    long overdue descriptions for scopDesc and ucscScop
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    50ca3c9a73d51d63bba6dd2bfee922f564a4ceee Wed Mar 13 07:42:50 2019 -0700
    oops, typo
• src/hg/lib/ucscScop.as
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    95575eb62326537cb3320ffe2857426cffa8241a Tue Mar 12 16:32:00 2019 -0700
    long overdue descriptions for scopDesc and ucscScop
• src/hg/makeDb/doc/hg38/mane.txt
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    a9bfddd1f195f8ca2c2cccad324c07a602804270 Wed Mar 13 15:31:37 2019 -0700
    add MANE track
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes18.sh
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    2698f5b2d4b7fab1aeb1f43c1b71e7c2ba60f70c Mon Mar 11 15:28:23 2019 -0700
    build the last few knownGene tables
• src/hg/makeDb/genbank/etc/gbPerAssemblyTables.txt
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    880b589d0be70548993b29d1711c52bb9ce45be2 Sat Mar 16 13:22:56 2019 -0700
    having ccdsKgMap as part of the standard release breaks things when UCSC genes is in flux
• src/hg/makeDb/schema/all.joiner
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    4783d0c1b81fdc972d42ef22f4e11d2cda16ab1d Thu Mar 14 14:30:43 2019 -0700
    exclude mm10 from having protein in knownCanonical
• src/hg/makeDb/trackDb/crisprAll.ra
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    2ae75276b78d694d04a7e2b10e156ec81cece10c Tue Mar 12 22:54:28 2019 -0700
    now showing crispr over entire genome refs #23047
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html
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    a93c23d6179e750da48ab655e0f0d8caaca21113 Wed Mar 13 10:23:44 2019 -0700
    Fixing broken link for nomLeu1, uiLinks cronjob
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html
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    a93c23d6179e750da48ab655e0f0d8caaca21113 Wed Mar 13 10:23:44 2019 -0700
    Fixing broken link for nomLeu1, uiLinks cronjob
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    fa016dafa20dadeb90add060d1d0fbf15c91da7a Wed Mar 13 04:50:02 2019 -0700
    putting masterming into a supertrack, refs #21895
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    5aad3f6bff6a4667e594c03f995f4236f9081172 Thu Mar 14 15:47:33 2019 -0700
    Editing hg19/trackDb.ra so mastermind track default visibilty is set to dense, refs #21895
• src/hg/makeDb/trackDb/human/hg19/varsInPubs.html
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    f0dac9fd4e2888a2edcdfc707b759540bccc8ad4 Mon Mar 18 07:04:30 2019 -0700
    docs page for varsInPubs supertracks, refs #21895
• src/hg/makeDb/trackDb/human/hg38/mane.html
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    3e7e186eb590a862fd2318e6466a6bfdb8ed7ee7 Thu Mar 14 12:13:51 2019 -0700
    some tweaks to the MANE track
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    4672e9a6a8a89ab0e9485dc4563f2ff7464fb786 Thu Mar 14 14:12:56 2019 -0700
    tweaks to MANE trackDb and html
• src/hg/makeDb/trackDb/human/hg38/mane.ra
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    a9bfddd1f195f8ca2c2cccad324c07a602804270 Wed Mar 13 15:31:37 2019 -0700
    add MANE track
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    3e7e186eb590a862fd2318e6466a6bfdb8ed7ee7 Thu Mar 14 12:13:51 2019 -0700
    some tweaks to the MANE track
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    4672e9a6a8a89ab0e9485dc4563f2ff7464fb786 Thu Mar 14 14:12:56 2019 -0700
    tweaks to MANE trackDb and html
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    37e583238de2ba79e96bf85e4e80e43df46ce754 Wed Mar 13 15:36:12 2019 -0700
    oops, mane needs a change to top-level trackDb.ra
• src/hg/makeDb/trackDb/makefile
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    6d4b033e2ce4813d455d6244b7908af15a8cfdf1 Wed Mar 13 10:43:03 2019 -0700
    initial files for perManBai1 refs #23111
• src/hg/makeDb/trackDb/mostConserved.html
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    8329acc95a92c72c5b7baccc1ad2a5400390dbc4 Tue Mar 12 09:20:29 2019 -0700
    Updating redirected links for monDom1, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/affyGnfU74A.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/affyGnfU74B.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/affyGnfU74C.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/genotypeArrays.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/gnfAtlas2.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/ikmc.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/NIAGene.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/allMm9RS_BW.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/exoniphy.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/knownGene.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/miRNA.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/polyASeqSites.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/pseudoYale60.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/rest.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/targetScanS.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/transcriptome.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
    Updating http to https for mouse (mm9). Also editing HTML lines to be less than 100 characters, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/vegaGeneComposite.html
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    6adc460ebdacd3f4ae2a593245db74be880ba275 Mon Mar 11 14:47:59 2019 -0700
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