All File Changes

v349_preview2 to v349_base (2017-05-08 to 2017-05-15) v349

• src/hg/cirm/cdw/cdwDumpManiFiles/cdwDumpManiFiles.c
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    cf8a6a49ccb1ffab0c0e8a76fa5ff22ad64fd9a0 Wed May 3 12:13:07 2017 -0700
    Made an error message for when you give it a bad dataSetId instead of just crashing.
• src/hg/cirm/cdw/cdwRunDaemon/cdwRunDaemon.c
  • lines changed 2, context: html, text, full: html, text
    073c968e7426e34b4f7e686dc9ffcaf6b7cf0ece Tue May 9 15:47:23 2017 -0700
    Renaming readAndIgnore to avoid conflict with library.
• src/hg/cirm/cdw/cdwWebBrowse/README_CSP
  • lines changed 16, context: html, text, full: html, text
    d54570617c4c51b04311f956961b2f58ff48b421 Wed May 10 16:11:19 2017 -0700
    Moving README_CSP to directory with the actually used cdwNavBar.h
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html
  • lines changed 41, context: html, text, full: html, text
    875ecc3fe29c3636516ee16010b0ecfa6d16e3f7 Wed May 10 16:07:21 2017 -0700
    Cleaning up cdwNavBar.h being in two places. Max moved it over to lib, and it is separate from the .html file now.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    c1828516b023ed36ed8fb50e4a0aa8a8e50f9f48 Mon May 8 15:25:57 2017 -0700
    updating dagre js lib url.
  • lines changed 1, context: html, text, full: html, text
    09695bbef6a32aa56f63e281e383fbe48bdeab74 Wed May 10 16:37:29 2017 -0700
    Making it so that the tagStormToHtml takes a nonce for CSP protection.
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 4, context: html, text, full: html, text
    875ecc3fe29c3636516ee16010b0ecfa6d16e3f7 Wed May 10 16:07:21 2017 -0700
    Cleaning up cdwNavBar.h being in two places. Max moved it over to lib, and it is separate from the .html file now.
• src/hg/cirm/cdw/lib/README_CSP
  • lines changed 16, context: html, text, full: html, text
    d54570617c4c51b04311f956961b2f58ff48b421 Wed May 10 16:11:19 2017 -0700
    Moving README_CSP to directory with the actually used cdwNavBar.h
• src/hg/cirm/cdw/lib/cdwNavBar.h
  • lines changed 6, context: html, text, full: html, text
    92b6a7326f55e8875bc1c15214b2097c41993995 Wed May 10 16:10:35 2017 -0700
    Fixing a CSP bug.
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    3deb44e4e36652d40e45ae6b3f5e4afb860d644c Wed May 3 12:42:56 2017 -0700
    make offering custom tracks with blat results the default
• src/hg/hgComposite/hgComposite.c
  • lines changed 6, context: html, text, full: html, text
    5199438a1019eff8b60a3f9bc404b6494ed800c2 Tue May 9 07:41:33 2017 -0700
    Add menus to do sorting on custom composites.
  • lines changed 1, context: html, text, full: html, text
    178bbf97e38aabf33f8e83308872e9548cc642e8 Tue May 9 07:52:59 2017 -0700
    add longLabel to track structure in hgComposite
  • lines changed 51, context: html, text, full: html, text
    6ecf4a7fdccf43addd6ca15bc2dedaa239852784 Tue May 9 16:09:07 2017 -0700
    ongoing work on hgComposite. Support add all visible button
  • lines changed 8, context: html, text, full: html, text
    9e30a2e3bce0cdb1bb4c4a0ddbd3325dfe9703ec Wed May 10 18:20:11 2017 -0700
    fix bug in handling of composites with views
  • lines changed 54, context: html, text, full: html, text
    402e9b52de6f531a9283c84bd20f91464517d3c7 Thu May 11 12:51:52 2017 -0700
    get "add all visible tracks" to work in hgComposite
  • lines changed 11, context: html, text, full: html, text
    985e22c1c56d7ba2909a96c1a66d8c4cff894340 Fri May 12 15:50:27 2017 -0700
    fix a bug in outputting large composites
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    48f55942e70c87801c7d0ad3a086765f3bfb6cbd Tue May 9 11:37:22 2017 -0700
    tell users about Hubs on CT pages. refs #19327
• src/hg/hgTables/custom.c
  • lines changed 12, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/hgTables/filterFields.c
  • lines changed 6, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/hgTables/hgTables.c
  • lines changed 5, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/hgTables/joining.c
  • lines changed 4, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/hgTables/schema.c
  • lines changed 7, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/hgTracks/hgTracks.c
  • lines changed 14, context: html, text, full: html, text
    f4ff89fd1ad92be8b97dc23a3a36829bb4e558c7 Mon May 8 13:48:10 2017 -0700
    add edit button on blue bar of user composites
  • lines changed 21, context: html, text, full: html, text
    5199438a1019eff8b60a3f9bc404b6494ed800c2 Tue May 9 07:41:33 2017 -0700
    Add menus to do sorting on custom composites.
• src/hg/hgTracks/imageV2.c
  • lines changed 3, context: html, text, full: html, text
    5199438a1019eff8b60a3f9bc404b6494ed800c2 Tue May 9 07:41:33 2017 -0700
    Add menus to do sorting on custom composites.
• src/hg/hgc/barChartClick.c
  • lines changed 5, context: html, text, full: html, text
    e472867f3de4f6f926d4e642220b85972815658a Tue May 9 09:28:11 2017 -0700
    More informative link for data points dataframe. refs #18736
  • lines changed 5, context: html, text, full: html, text
    c55e112ffa131f0a5999f22b4eabd0178b50492e Tue May 9 10:30:54 2017 -0700
    Add setting barChartMatrixUrl. Will replace barChartDataUrl (left in for now for internal user/QA convenience. Also fixed broken links in trackDb docs. refs #18736
• src/hg/hgc/hgc.c
  • lines changed 193, context: html, text, full: html, text
    032ef09c0d89b90b4967379956b2f8d9446575b9 Thu May 11 11:05:18 2017 -0700
    Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919
  • lines changed 193, context: html, text, full: html, text
    2a20896498b6edf0c19565c8f8a19b29326da08c Thu May 11 11:38:52 2017 -0700
    Putting COSMIC code back into hgc.c will remove again later, refs #14461
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 706, context: html, text, full: html, text
    e84e946222de57e30a4082c55db1b923906ba434 Mon May 8 20:57:02 2017 -0700
    First pass at updating this file. Will flip it to current style after we've decided how we want to proceed with it. Refs #18504
• src/hg/htdocs/goldenPath/help/compositeHelp.html
  • lines changed 7, context: html, text, full: html, text
    a55e58153bee565c9f301c9dae0c37a6b11d1345 Mon May 8 17:38:09 2017 -0700
    Renaming hgComposite help page to fit with our standards, refs #11630
  • lines changed 82, context: html, text, full: html, text
    1c8494bd603fe443797afabf17ca6c7ff6c5b34c Mon May 8 18:10:59 2017 -0700
    Just adding roughdraft placeholders for hgComposite help, refs #11630
  • lines changed 86, context: html, text, full: html, text
    e0e4c711a02f455ddf7052dcbf90dbe45f995fb5 Mon May 8 18:12:19 2017 -0700
    Renaming hgComposite help page to fit with our standards, meant to keep the 'hg' refs #11630
• src/hg/htdocs/goldenPath/help/customTrackManage.html
  • lines changed 6, context: html, text, full: html, text
    4fd0306de83620dc7b7184b26f3907e151c3abe5 Tue May 9 11:45:50 2017 -0700
    tell users about Hubs on CT pages. refs #19327
• src/hg/htdocs/goldenPath/help/hgCompositeHelp.html
  • lines changed 86, context: html, text, full: html, text
    e0e4c711a02f455ddf7052dcbf90dbe45f995fb5 Mon May 8 18:12:19 2017 -0700
    Renaming hgComposite help page to fit with our standards, meant to keep the 'hg' refs #11630
  • lines changed 99, context: html, text, full: html, text
    57c9c4ce8429aacc4189030fd4baaf5ccdd4a520 Tue May 9 15:49:24 2017 -0700
    Beefing up the 1st draft of hgCompositeHelp, refs #11630
  • lines changed 39, context: html, text, full: html, text
    e898b0d0f16ee8e072216965e8b59bf4887df6d1 Tue May 9 17:32:24 2017 -0700
    Minor edits on 1st draft of hgCompositeHelp, refs #11630
  • lines changed 1, context: html, text, full: html, text
    850119d0469a33500730872440681514749d4248 Tue May 9 17:42:44 2017 -0700
    Fixing CB url on 1st draft of hgCompositeHelp, refs #11630
  • lines changed 44, context: html, text, full: html, text
    ab68188568bf5b0665ff690aac58df61fea9f6e7 Fri May 12 14:56:41 2017 -0700
    Saving rough draft changes to hgCompositeHelp, refs #11630
• src/hg/htdocs/goldenPath/help/hgCompositeHelpText.html
  • lines changed 7, context: html, text, full: html, text
    a55e58153bee565c9f301c9dae0c37a6b11d1345 Mon May 8 17:38:09 2017 -0700
    Renaming hgComposite help page to fit with our standards, refs #11630
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 77, context: html, text, full: html, text
    2c12b763bd4a9dcf47e84b7162cd2047a93c092f Wed May 10 14:18:06 2017 -0700
    Formatting changes to hgGeneGraph help page. Changed anchor names for each section. Changed incorrectly formatted characters that resulted from copying text over from Google Docs. refs #13634
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    086d0187a362acf4ecd03b0a93a2888f4990034c Wed May 10 12:32:54 2017 -0700
    Fixing minor typo, refs #19370
• src/hg/htdocs/goldenPath/help/phastCons.html
  • lines changed 0, context: html, text, full: html, text
    7f939e51f3717a0fda0e37dfa8ed998a85743d5b Tue May 9 11:48:23 2017 -0700
    Fixed typo reported by Luvina. Refs #19365
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    c55e112ffa131f0a5999f22b4eabd0178b50492e Tue May 9 10:30:54 2017 -0700
    Add setting barChartMatrixUrl. Will replace barChartDataUrl (left in for now for internal user/QA convenience. Also fixed broken links in trackDb docs. refs #18736
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 5, context: html, text, full: html, text
    c55e112ffa131f0a5999f22b4eabd0178b50492e Tue May 9 10:30:54 2017 -0700
    Add setting barChartMatrixUrl. Will replace barChartDataUrl (left in for now for internal user/QA convenience. Also fixed broken links in trackDb docs. refs #18736
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    c55e112ffa131f0a5999f22b4eabd0178b50492e Tue May 9 10:30:54 2017 -0700
    Add setting barChartMatrixUrl. Will replace barChartDataUrl (left in for now for internal user/QA convenience. Also fixed broken links in trackDb docs. refs #18736
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    7ecb2d8efe225d140cb50cd29528173b20af35a8 Tue May 9 12:21:44 2017 -0700
    Changes from code review, refs #19366
  • lines changed 3, context: html, text, full: html, text
    086d0187a362acf4ecd03b0a93a2888f4990034c Wed May 10 12:32:54 2017 -0700
    Fixing minor typo, refs #19370
  • lines changed 23, context: html, text, full: html, text
    d2a1a2b1db4ecb3fa94e330f3af2f9131297e26f Mon May 15 08:47:58 2017 -0700
    Adding announcement for TransMap V4 tracks. Also tweaked titles for a dew previous releases as they were missing the white used in previous announcements. refs #18818
  • lines changed 1, context: html, text, full: html, text
    35dcdf443c4451f6ecab3279659ed0236fe26bc9 Mon May 15 08:52:40 2017 -0700
    Minor type correction, refs #18818
• src/hg/htdocs/images/hpv1.jpg
  • lines changed 0, context: html, text, full: html, text
    a3d4d044a2c0d48a13792ba44b781439b64dec6a Wed May 10 11:27:12 2017 -0700
    from: NIH National Cancer Institute via https://commons.wikimedia.org/wiki/File:Papilloma_virus_(hpv).jpg refs #18971
• src/hg/htdocs/images/phylo/hpv1_47way.png
  • lines changed 0, context: html, text, full: html, text
    4b807dd1a1bde4abc5c02e3788aeadce8fc9e81d Sun May 14 22:07:01 2017 -0700
    47-way diagram for HPV1 refs #18971
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    d2a1a2b1db4ecb3fa94e330f3af2f9131297e26f Mon May 15 08:47:58 2017 -0700
    Adding announcement for TransMap V4 tracks. Also tweaked titles for a dew previous releases as they were missing the white used in previous announcements. refs #18818
• src/hg/inc/barChartBed.h
  • lines changed 3, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/inc/hCommon.h
  • lines changed 3, context: html, text, full: html, text
    f4ff89fd1ad92be8b97dc23a3a36829bb4e558c7 Mon May 8 13:48:10 2017 -0700
    add edit button on blue bar of user composites
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    ba9d5d0321eac8766a88194623cbd51b46b34d0d Mon May 15 09:59:09 2017 -0700
    New version number v349
• src/hg/js/hgTracks.js
  • lines changed 39, context: html, text, full: html, text
    5199438a1019eff8b60a3f9bc404b6494ed800c2 Tue May 9 07:41:33 2017 -0700
    Add menus to do sorting on custom composites.
• src/hg/lib/barChartBed.c
  • lines changed 26, context: html, text, full: html, text
    e2e920776dddac39896fdb4aebae84a12bcb52b1 Tue May 9 11:06:33 2017 -0700
    Add table browwser support for barChart custom tracks. refs #18736
• src/hg/lib/cosmicNew.as
  • lines changed 30, context: html, text, full: html, text
    032ef09c0d89b90b4967379956b2f8d9446575b9 Thu May 11 11:05:18 2017 -0700
    Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919
• src/hg/lib/ggDoc.as
  • lines changed 13, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
• src/hg/lib/ggDocEvent.as
  • lines changed 6, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
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    034ef706506d6ec55823be823a5450e2adaa598b Fri May 12 11:33:15 2017 -0700
    fixing two .as files, refs #13634
• src/hg/lib/ggEvent.as
  • lines changed 10, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
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    c40d723b560123b36d4f3dd1b4e489c761b35e17 Sun May 14 11:05:18 2017 -0700
    fixing another .as error found by the nightly checker
• src/hg/lib/ggEventDb.as
  • lines changed 17, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
• src/hg/lib/ggEventText.as
  • lines changed 21, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
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    cafa46fea4e494c531d1d6e1c1f62a4a95e8927e Sun May 14 11:08:07 2017 -0700
    ...and another .as fix...
• src/hg/lib/ggGeneClass.as
  • lines changed 6, context: html, text, full: html, text
    f0629a14aa9fc291af54385b5d2b960e0f785f9f Thu May 11 16:05:55 2017 -0700
    adding two more .as files, refs #13634
• src/hg/lib/ggGeneName.as
  • lines changed 7, context: html, text, full: html, text
    f0629a14aa9fc291af54385b5d2b960e0f785f9f Thu May 11 16:05:55 2017 -0700
    adding two more .as files, refs #13634
• src/hg/lib/ggLink.as
  • lines changed 14, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
• src/hg/lib/ggLinkEvent.as
  • lines changed 7, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
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    034ef706506d6ec55823be823a5450e2adaa598b Fri May 12 11:33:15 2017 -0700
    fixing two .as files, refs #13634
• src/hg/lib/gglinkEvents.as
  • lines changed 7, context: html, text, full: html, text
    7f5a39fa7ecbf668c7ec0cc077dc7b7821fae06c Thu May 11 15:27:16 2017 -0700
    adding .as files for interactions tracks, refs #13634
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    5e5df046911fbca080c8525111b214ec1d849c9f Sat May 13 08:35:20 2017 -0700
    removing stray .as file
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    f4ff89fd1ad92be8b97dc23a3a36829bb4e558c7 Mon May 8 13:48:10 2017 -0700
    add edit button on blue bar of user composites
• src/hg/lib/hgHgvs.c
  • lines changed 45, context: html, text, full: html, text
    cc6ca259385f385c252b6a675801025e96783818 Thu May 11 12:40:15 2017 -0700
    Converting HGVS coords to 0-based needs to be done differently when the HGVS coords are negative because when negative they are already 0-based (but end is closed and needs to be converted to open). fixes #19396
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    2bff6bdbbce7e4ef57b27d4104a12a076dc90ca5 Fri May 12 14:12:45 2017 -0700
    gbSeqTable doesn't work as compatTable for hGenBankGet* -- wrong columns. Also recognize indel when no-change in HGVS transcript term aligns to a deletion in reference. We're not yet showing the correct alt sequence in that case.
• src/hg/lib/hui.c
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    d29ef4ffcf1e5fcd00755acea404bb42633fa71b Tue May 9 09:42:55 2017 -0700
    Fix bug in last update time noted in code review (tnx Max!). refs #18736
• src/hg/makeDb/crisprTrack/catAndIndex
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    f38d906b034d7666623cd21d1f66a75e802ad779 Thu May 11 14:54:07 2017 -0700
    adding missing catAndIndex to source tree, thanks Hiram, refs #18968
• src/hg/makeDb/crisprTrack/convOffs.py
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    dc1d241ad9b7b104a3bd8d9965f036046dc934fe Tue May 9 17:17:45 2017 -0700
    fixing doCrispr script for Regeneron
• src/hg/makeDb/crisprTrack/createBigBed.py
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    dbdb6c3289973ab77712343bcf30d8296e9f3ef3 Tue May 9 10:23:02 2017 -0700
    fixes after code review, refs #19358
• src/hg/makeDb/crisprTrack/crisprAddGenome.py
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    a5f55498675912016c945acd791be4128341f350 Tue May 9 13:48:25 2017 -0700
    imported script from the git hub refs #18968
• src/hg/makeDb/crisprTrack/doCrispr.sh
  • lines changed 3, context: html, text, full: html, text
    dc1d241ad9b7b104a3bd8d9965f036046dc934fe Tue May 9 17:17:45 2017 -0700
    fixing doCrispr script for Regeneron
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    e17cdab1a049971db0b3f184d989b6efc7d04ba5 Thu May 11 14:55:46 2017 -0700
    fixing doCrispr.sh, refs #18968
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    e14d0f43abf023b6311bf63ab0411a1969d43291 Fri May 12 09:50:18 2017 -0700
    tiny fix to doCrispr, after feedback from Hiram
• src/hg/makeDb/doc/aquChr2/initialBuild.txt
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    b6a22c9242b039dc11b4e30378dfbad356f0edf5 Tue May 9 15:26:40 2017 -0700
    adding blat servers refs #15096
• src/hg/makeDb/doc/ci3/initialBuild.txt
  • lines changed 120, context: html, text, full: html, text
    9696526fdb03bf1abb90a0c6a91db36b0181db36 Tue May 9 11:19:33 2017 -0700
    adding blat servers refs #16628
• src/hg/makeDb/doc/criGri1.txt
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    17d8c4c98bf3668bf19c8562ca36f11522e3ed32 Fri May 12 10:30:59 2017 -0700
    new default position from Regeneron recommendation refs #19228
• src/hg/makeDb/doc/criGriChoV1/initialBuild.txt
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    3fd1fd8a1a68b38acdaad9ce8c44048d44ac06d8 Fri May 12 09:29:36 2017 -0700
    new default position recommendation from regeneron refs #19228
• src/hg/makeDb/doc/hg19.txt
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    032ef09c0d89b90b4967379956b2f8d9446575b9 Thu May 11 11:05:18 2017 -0700
    Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919
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    9c6973bc64e6f6d22bfe1d6afe5dec4f81fe4c2b Fri May 12 08:24:53 2017 -0700
    panTro5 hg19 chainNet per user request refs #19343
• src/hg/makeDb/doc/hg38/hg38.txt
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    032ef09c0d89b90b4967379956b2f8d9446575b9 Thu May 11 11:05:18 2017 -0700
    Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919
• src/hg/makeDb/doc/hpv1/initialBuild.txt
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    3a340242689d5e3c1843c38a897f147f68e6fb72 Wed May 10 16:31:19 2017 -0700
    done with masking refs #18971
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    0334129bbf3460f87cde95e8e25eedcf7f440e22 Fri May 12 08:20:51 2017 -0700
    genbank loaded nothing ? refs #18971
• src/hg/makeDb/doc/panTro5/lastzRuns.txt
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    9c6973bc64e6f6d22bfe1d6afe5dec4f81fe4c2b Fri May 12 08:24:53 2017 -0700
    panTro5 hg19 chainNet per user request refs #19343
• src/hg/makeDb/genbank/etc/genbank.conf
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    88b767d53c72fb363d33b118dfe46cbe6450c931 Wed May 10 18:34:17 2017 -0700
    adding hpv1 Human papillomavirus type 90 - refs #18971
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    da7163da71118bdc8a4a1cff41a53386bbe5c35a Tue May 9 14:24:42 2017 -0700
    Turning on Genbank updates for Golden eagle on hgwbeta, refs #15096
• src/hg/makeDb/genbank/etc/rr.dbs
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    b55b27ee36607c9a4b1d8f48f0f9f454354075d0 Fri May 12 14:08:19 2017 -0700
    Turning on Genbank updates for aquChr2 on the RR, refs #15096
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    88b767d53c72fb363d33b118dfe46cbe6450c931 Wed May 10 18:34:17 2017 -0700
    adding hpv1 Human papillomavirus type 90 - refs #18971
• src/hg/makeDb/schema/all.joiner
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    84dba5bd375f9fe037ae695886b6ca82ce5cceb6 Mon May 8 10:24:36 2017 -0700
    adding chrPic2 rules and eliminate duplicate check for chainId refs #13166
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    a78ec0caef7d1fb397793f347bf6a5fb581de2bf Mon May 8 13:18:10 2017 -0700
    the chainId rule needs to be there causes duplicate checks refs #13166
• src/hg/makeDb/trackDb/HPV/hpv1/description.html
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    67dc46bec08d36858fd06f48a6c8735812e2c44d Wed May 10 11:41:04 2017 -0700
    initial files from makeGenomeDb.pl refs #18971
• src/hg/makeDb/trackDb/HPV/hpv1/gap.html
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    67dc46bec08d36858fd06f48a6c8735812e2c44d Wed May 10 11:41:04 2017 -0700
    initial files from makeGenomeDb.pl refs #18971
• src/hg/makeDb/trackDb/HPV/hpv1/gold.html
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    67dc46bec08d36858fd06f48a6c8735812e2c44d Wed May 10 11:41:04 2017 -0700
    initial files from makeGenomeDb.pl refs #18971
• src/hg/makeDb/trackDb/HPV/hpv1/trackDb.ra
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    67dc46bec08d36858fd06f48a6c8735812e2c44d Wed May 10 11:41:04 2017 -0700
    initial files from makeGenomeDb.pl refs #18971
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    a76c2ddec0804734fc3c2cfa1bce1b567456a2e0 Wed May 10 13:17:45 2017 -0700
    add gold search rule refs #18971
• src/hg/makeDb/trackDb/birds/aquChr2/trackDb.chainNet.ra
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    d2d069e4b03733f9497386a26ff7bbe645c8a5d0 Mon May 8 16:19:53 2017 -0700
    Turning Genscan and the Chicken chain/nets on by default for the aquChr2 Genome Browser, refs #15096
• src/hg/makeDb/trackDb/birds/aquChr2/trackDb.ra
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    d2d069e4b03733f9497386a26ff7bbe645c8a5d0 Mon May 8 16:19:53 2017 -0700
    Turning Genscan and the Chicken chain/nets on by default for the aquChr2 Genome Browser, refs #15096
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
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    1f0b027a3b27bb19bbf97cc3381e17e1ca4be6b2 Fri May 12 09:51:53 2017 -0700
    reset default visibilities on recommendation from Regeneron refs #19228
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
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    e1f54d18c644fb90aaeb915f241106a6ba02c229 Tue May 9 13:16:09 2017 -0700
    Overrides to change default tracks and to include correct chainMinScore/LinearGap, refs #19228
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    1f0b027a3b27bb19bbf97cc3381e17e1ca4be6b2 Fri May 12 09:51:53 2017 -0700
    reset default visibilities on recommendation from Regeneron refs #19228
• src/hg/makeDb/trackDb/gorilla/gorGor5/description.html
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    06f13b0068b06c777df610e4015b8b8ee567efe2 Mon May 8 14:17:17 2017 -0700
    Corrected weird capitalization for University of WA.
• src/hg/makeDb/trackDb/human/chainNetMelGal1.ra
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    3144c63365cc4508559aeba3007e197747878f78 Wed May 10 11:03:58 2017 -0700
    To contain turkey (melGal1) on hg19 adding an include statement and new human/chainNetMelGal1.ra file, this works for beta/RR, on dev melGal1 will still be loose refs #11681
• src/hg/makeDb/trackDb/human/cosmicRegions.html
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    032ef09c0d89b90b4967379956b2f8d9446575b9 Thu May 11 11:05:18 2017 -0700
    Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
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    3144c63365cc4508559aeba3007e197747878f78 Wed May 10 11:03:58 2017 -0700
    To contain turkey (melGal1) on hg19 adding an include statement and new human/chainNetMelGal1.ra file, this works for beta/RR, on dev melGal1 will still be loose refs #11681
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    f2579abb28b01318b0ec95fe3d54731180fadac8 Thu May 11 11:09:53 2017 -0700
    Cosmic tracks trackDb changes, refs #14461 and #18919
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    f2579abb28b01318b0ec95fe3d54731180fadac8 Thu May 11 11:09:53 2017 -0700
    Cosmic tracks trackDb changes, refs #14461 and #18919
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    89a644fbb29ca0bede54ee1b3081c2431dedd22c Mon May 8 14:01:12 2017 -0700
    Update track labeling... getting ready for newer data. refs #18332
• src/hg/makeDb/trackDb/human/trackDb.ra
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    572c129a92e7b5d4c3734d0220113ea11cd16371 Fri May 12 08:14:06 2017 -0700
    Completing Data Access section. Making links on page open in new tabs/windows. Changing track shortLabel to fit within our limitations. Moving track to Phenotype and Literature group. refs #13634
• src/hg/makeDb/trackDb/interactions.html
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    efb71022027eedc7a857ea5781e258eb8874949c Wed May 10 14:13:15 2017 -0700
    Adding track description page for Max's new Protein Interactions track, refs #13634
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    572c129a92e7b5d4c3734d0220113ea11cd16371 Fri May 12 08:14:06 2017 -0700
    Completing Data Access section. Making links on page open in new tabs/windows. Changing track shortLabel to fit within our limitations. Moving track to Phenotype and Literature group. refs #13634
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    0bc117ca00002650e534a974c0a15a8a32022fee Fri May 12 08:38:53 2017 -0700
    Removing redundant part of sentence about downloading bigBedToBed, refs #13634
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
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    2eb8caae32eb893b1be6852a2ebd46c74f485d6c Thu May 11 14:47:59 2017 -0700
    Changing the GENCODE VM11 track set to pack by default in the GENCODE super-track for mm10, refs #19187
• src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra
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    eaf7e69b8a84ac9fe58ad3a3bb659ff70f9672cc Tue May 9 14:58:36 2017 -0700
    Making the SNP(126) the first default track in the Variation and Repeats group for mm8, refs #19187
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
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    8f19502b126f85cebfdc4110e6719a7408f97803 Tue May 9 14:48:21 2017 -0700
    Making the SNP(128) track the first default track in the Variation and Repeats group for mm9, refs #19187
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
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    11c87d0872d80bdf844d0e640f95e574da8ea871 Tue May 9 14:39:22 2017 -0700
    Sorting the Comparative Genomics group by phylogenetic order, refs #19187
• src/hg/makeDb/trackDb/tagTypes.tab
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    c55e112ffa131f0a5999f22b4eabd0178b50492e Tue May 9 10:30:54 2017 -0700
    Add setting barChartMatrixUrl. Will replace barChartDataUrl (left in for now for internal user/QA convenience. Also fixed broken links in trackDb docs. refs #18736
• src/hg/utils/automation/cosmicToBed
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    032ef09c0d89b90b4967379956b2f8d9446575b9 Thu May 11 11:05:18 2017 -0700
    Cosmic tracks scripts, code changes and documentation, refs #14461 and #18919
• src/hg/utils/automation/doBlastzChainNet.pl
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    0aadfe099a9b23771fb238be21aa8c31bb82cf9a Fri May 12 09:22:09 2017 -0700
    changing blastz to lastz on README references refs #19343
• src/hg/utils/automation/makeGenomeDb.pl
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    8f070a0b99b2a397d2be0215198089930272cf6f Wed May 10 11:39:13 2017 -0700
    eliminate bogus </I> tag refs #18971
• src/hg/utils/hgvsToVcf/hgvsToVcf.c
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    b7b52acb53114733301bf8fd23d269c6178518ab Fri May 12 14:08:54 2017 -0700
    Oops, hgvsToVcf (and any program that needs RefSeq/GenBank stuff) needs to call initGenbankTableNames().
• src/hg/utils/hubCrawl/hubCrawl.c
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    932cada2ceba46cf9af7d0dca3057973376b5e34 Mon May 8 13:49:57 2017 -0700
    Fix crash in hubCrawl if descriptionUrl cannot be opened.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    2ecfffc3309bd1cdffe79378ac24a73d1832f0f5 Mon May 8 11:53:16 2017 -0700
    Should perform faster since most settings in a saved cart do not need to be decoded.
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    1dbb921507c9f41988f5b9a8f806eddeca1de6e0 Tue May 9 10:48:54 2017 -0700
    recognize hgComposite trash files and no need to read files to touch them refs #11630
• src/lib/htmshell.c
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    6b4966bc5eca52a5200fd6997192ee1b05a5e996 Mon May 8 15:19:14 2017 -0700
    adding/updating cirm js libs.
• src/lib/net.c
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    c245527d873cab1c31955059259a405a67badc4b Wed May 10 11:25:57 2017 -0700
    oops those are signed so that -1 can represent a missing value as in an unspecified range end, which means get everything up to the end of the file.
• src/lib/udc.c
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    5d25b7b10a486fb25edff4391db1c02cb70fb416 Wed May 10 11:23:50 2017 -0700
    I never found evidence that the URL was coming in with a byterange clause appended to it.
• src/oneShot/sqlToAs/sqlToAs
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    891f9aeae5e65a5d5ff107479b1f5830b67312c5 Thu May 11 15:54:47 2017 -0700
    small fix to sqlToAs, for interactions track
• src/product/ex.hg.conf
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    f3dcc9ef6076abb60e849af5dfc8731ea63fe32b Wed May 10 16:33:55 2017 -0700
    documentation hg.conf option used by hgGeneGraph for ChrisL
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    19d59a7c4442e20f0ce3cf6d58cca73e72587abc Wed May 10 16:45:23 2017 -0700
    Adding blat custom track hg.conf option to example hg.conf for mirrors, refs #2811
• src/product/installer/browserSetup.sh
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    2b3f56043a62c8cd668a8a51016e47e4fc7f8c4a Mon May 8 16:50:14 2017 -0700
    fixing missing R-core package from redhat'ish install in gbic, refs #19380
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    4fd61e3af4dec35b8b177d327596910acbce1cc8 Tue May 9 11:41:53 2017 -0700
    Fixing r installation for redhat mirrors, refs #19380
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    3896e8dcb9cb0cc934009e8f8c265b084da5a237 Tue May 9 11:54:40 2017 -0700
    fixing centos install on gbic, refs #19380
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    45ea37a7c30d74ae3bab8a6e72b421f36c0a18e3 Tue May 9 13:46:12 2017 -0700
    removing -s from read in gbic, refs #19380
• src/product/minimal.hg.conf
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    c6c7bbc5c33cb88be80c2411edb4724ab46e0e97 Mon May 15 09:38:57 2017 -0700
    Adding gbdbLoc lines to minimal hg.conf for vai.pl usage, refs #12216
• src/tagStorm/tagStormToHtml/tagStormToHtml.c
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    13ac54c9adfa0981b03f95d63e7b49f9c42b373d Mon May 8 13:34:55 2017 -0700
    Rearranging so that each stanza is a separate LI. This will be a tiny bit slower, but I think worth it for the clarity of having the stanza hilight on mous over rather than the whole level.
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    7abe4cd1e2a6173528f783090027ad37fb8a9a32 Wed May 10 16:37:53 2017 -0700
    Making it so that the tagStormToHtml takes a nonce for CSP protection.
• src/utils/bedOverlapMerge
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    634275bbaa417bb81e44cca7aaa1757ee7b57b82 Fri May 12 11:19:51 2017 -0700
    fixing up crispr track pipeline for CHO/Hiram
• src/utils/doLocusName
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    634275bbaa417bb81e44cca7aaa1757ee7b57b82 Fri May 12 11:19:51 2017 -0700
    fixing up crispr track pipeline for CHO/Hiram
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    0502f1581f13bae7ba257fc290176d64e8bfd616 Wed May 10 15:25:52 2017 -0700
    Changing the format of one of the input files and updating documentation a bit, refs #19155
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    56e1d09dbeac2c8233ef0ca36541e937a068c8aa Fri May 12 10:30:32 2017 -0700
    Fixing up the usage statement, refs #19155
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    cf97b091f2c45ee59d6b242095ba02bec724c37f Fri May 12 12:58:38 2017 -0700
    Fixing an error with column order and a syntax error with a print statement, refs #19155
• src/utils/expMatrixToBarchartBed/tests/test.coords
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    0502f1581f13bae7ba257fc290176d64e8bfd616 Wed May 10 15:25:52 2017 -0700
    Changing the format of one of the input files and updating documentation a bit, refs #19155
• src/utils/expMatrixToBarchartBed/tests/test.output
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    0502f1581f13bae7ba257fc290176d64e8bfd616 Wed May 10 15:25:52 2017 -0700
    Changing the format of one of the input files and updating documentation a bit, refs #19155
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    cf97b091f2c45ee59d6b242095ba02bec724c37f Fri May 12 12:58:38 2017 -0700
    Fixing an error with column order and a syntax error with a print statement, refs #19155
• src/utils/expMatrixToBarchartBed/tests/test.output2
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    0502f1581f13bae7ba257fc290176d64e8bfd616 Wed May 10 15:25:52 2017 -0700
    Changing the format of one of the input files and updating documentation a bit, refs #19155
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    cf97b091f2c45ee59d6b242095ba02bec724c37f Fri May 12 12:58:38 2017 -0700
    Fixing an error with column order and a syntax error with a print statement, refs #19155
• src/utils/qa/weeklybld/buildEnv.csh
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    863b311f26403a3d457d75a732d8c69a55bb4bbb Mon May 15 09:58:18 2017 -0700
    v349 final build refs #19342
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
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    dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/doLiftOverTestRobot.csh
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    dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/doNewReview.csh
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    dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/doNewReview2.csh
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    dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/doTrackCheckRobot.csh
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    dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/makeStrictBeta.csh
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    1044a6388a242b7007db966548bd8fc3e713407b Tue May 9 14:53:33 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
• src/utils/qa/weeklybld/moveBranchTag.csh
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    1044a6388a242b7007db966548bd8fc3e713407b Tue May 9 14:53:33 2017 -0700
    there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine

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