File Changes for hiram

v376_preview to v376_preview2 (2018-12-17 to 2019-01-07) v376

• src/hg/hgTracks/wigMafTrack.c
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    081e0431f88cf0536f1c4c56e56c3a0007890ab0 Wed Jan 2 13:20:26 2019 -0800
    speed up display for codonDefault AA display refs #19937
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    c8da620b1e51e27548201a8f4aa16bbc4d9aaecc Mon Jan 7 10:13:30 2019 -0800
    add to comment about speed up display refs #19937
• src/hg/htdocs/images/Eulemur_flavifrons,jpg
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    2f39747123c131d22d82f2bc661fb6a82f3a658e Thu Jan 3 13:13:07 2019 -0800
    remove bogus file name with comma in place of period no redmine
• src/hg/lib/cart.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/lib/jksql.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/lib/snpTmp.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/lib/wigDataStream.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/makeDb/doc/bosTau6.txt
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    43c2ea2c14ffb39612182c7f98170f604ddf22ca Fri Dec 21 15:33:40 2018 -0800
    liftOvers to bosTau9 per user request refs #22399
• src/hg/makeDb/doc/bosTau7.txt
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    43c2ea2c14ffb39612182c7f98170f604ddf22ca Fri Dec 21 15:33:40 2018 -0800
    liftOvers to bosTau9 per user request refs #22399
• src/hg/makeDb/doc/bosTau8.txt
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    43c2ea2c14ffb39612182c7f98170f604ddf22ca Fri Dec 21 15:33:40 2018 -0800
    liftOvers to bosTau9 per user request refs #22399
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
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    f566f5f02dc7339e212d88659d811aed488c5fc8 Fri Dec 21 15:34:51 2018 -0800
    bosTau9 browser build done refs #22425
• src/hg/makeDb/doc/ce11/multiz135way.txt
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    1b14bc9f8f21671b91d698b48fcee080d668a2e1 Fri Dec 21 15:27:54 2018 -0800
    track complete QA Ready refs #22599
• src/hg/makeDb/doc/dm6/multiz124way.txt
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    b9e2880b0c244b4118ea0c1b445119cf7016e3a6 Wed Dec 19 16:03:01 2018 -0800
    restart multiz with new phylo tree refs @22550
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    1257fd0a18976f8dce7ba049cd5494285504fcfc Fri Dec 21 15:25:29 2018 -0800
    rework this track with a better phylo tree refs #22550
• src/hg/makeDb/doc/galGal6/initialBuild.txt
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    cf8e0c3e1c2ae902fe4acc06cfbfb08a0627a5d2 Fri Dec 21 15:37:41 2018 -0800
    finished cotJap2 lastz/chainNet and browser build complete refs #22113
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
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    cf8e0c3e1c2ae902fe4acc06cfbfb08a0627a5d2 Fri Dec 21 15:37:41 2018 -0800
    finished cotJap2 lastz/chainNet and browser build complete refs #22113
• src/hg/makeDb/doc/galGal6/multiz77way.txt
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    d3982d16735c2ac591fe480ae3775f417be29d6c Fri Dec 21 15:26:52 2018 -0800
    done with this track marked QA Ready refs #22687
• src/hg/makeDb/doc/hg19.txt
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    2d27a24738cb880e57505cd71605072629c05368 Fri Dec 21 15:31:24 2018 -0800
    panTro6 and ponAbe3 liftOvers per user request refs #2657
• src/hg/makeDb/doc/hg38/crispr.txt
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    f82654e4d16d4911e236d3e8faad58bd1b9b765b Fri Dec 21 15:38:38 2018 -0800
    completed 10K track refs #21575
• src/hg/makeDb/doc/petMar2.txt
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    acdf58105d537fdcadff7a5f1dbaceebe1869dfe Fri Dec 21 15:42:21 2018 -0800
    liftOver to petMar3 for petMar3 browser release refs #20819
• src/hg/makeDb/doc/rn6.txt
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    d90aaacb8b2c810a3689b8cd7f27ace9bd55d76b Fri Dec 21 15:57:17 2018 -0800
    running up crispr 10K to test fixes to the script refs #21987
• src/hg/makeDb/doc/staAur2/compositeTrack.sh
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    c794f73d6f86f6d33fc75d10240eee1b6dcb1cbc Mon Dec 31 12:30:23 2018 -0800
    initial scripts to count mafGene AAs and construct AA profile composite track refs #19937
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    64636f495149ba1e1d52b785645d8fe4dbab3d00 Mon Dec 31 12:31:33 2018 -0800
    AA composite track now with mouse over data and color coding frequency refs #19937
• src/hg/makeDb/doc/staAur2/geneDescScan.pl
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    9bf992fff5f52b6c8f915bb868f2d01d21cd7ce3 Thu Jan 3 15:50:24 2019 -0800
    script used to scan the gene definitions extracting descriptions for clicks on ncbiGene track refs #19937
• src/hg/makeDb/doc/staAur2/initialBuild.txt
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    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
    initial browser build and 369-way alignment up thru i-row annotation refs #19937
• src/hg/makeDb/doc/staAur2/matrixUp.pl
  • lines changed 70, context: html, text, full: html, text
    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
    initial browser build and 369-way alignment up thru i-row annotation refs #19937
• src/hg/makeDb/doc/staAur2/multiz369way.txt
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    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
    initial browser build and 369-way alignment up thru i-row annotation refs #19937
• src/hg/makeDb/doc/staAur2/scanExonAA.pl
  • lines changed 239, context: html, text, full: html, text
    c794f73d6f86f6d33fc75d10240eee1b6dcb1cbc Mon Dec 31 12:30:23 2018 -0800
    initial scripts to count mafGene AAs and construct AA profile composite track refs #19937
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    64636f495149ba1e1d52b785645d8fe4dbab3d00 Mon Dec 31 12:31:33 2018 -0800
    AA composite track now with mouse over data and color coding frequency refs #19937
• src/hg/makeDb/doc/staAur2/staAur2.369way.nh
  • lines changed 369, context: html, text, full: html, text
    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
    initial browser build and 369-way alignment up thru i-row annotation refs #19937
• src/hg/makeDb/genbank/etc/genbank.conf
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    28690c391977a93ec08c0abda3fefb029a4b2d32 Wed Jan 2 16:21:35 2019 -0800
    adding staAur2 Staphylococcus aureus- refs #19937
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    a6015a4f939b89fae9a99fb379d6ab5975be4f38 Wed Jan 2 16:24:53 2019 -0800
    Added staAur2 - Staphylococcus aureus refs #19937
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    28690c391977a93ec08c0abda3fefb029a4b2d32 Wed Jan 2 16:21:35 2019 -0800
    adding staAur2 Staphylococcus aureus- refs #19937
• src/hg/makeDb/schema/all.joiner
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    3a4ae2296f5def3c5d9d0fecf3c1971843249da3 Thu Jan 3 14:03:29 2019 -0800
    adding staAur2 rules refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/aaCounts.ra
  • lines changed 191, context: html, text, full: html, text
    a686a883905d058d863c2b7b277f009864a6820c Mon Dec 31 00:59:19 2018 -0800
    adding composite track of AA profiles refs #19937
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    d5a6f8527eda49f3f45aa5e5e0794ffdde7e30e5 Mon Dec 31 11:53:19 2018 -0800
    now with mouse over information refs #19937
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    79a63f79023731177747e95e2fe8a75bbb152131 Mon Dec 31 18:38:24 2018 -0800
    rmsk default off and adjusting ordering of tracks in aaCounts refs #19937
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    f8a6772a141e5503918a6fea0d709b57f2d0944e Thu Jan 3 13:09:53 2019 -0800
    correct two dimensions and labelOnFeature off everywhere refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/chainNetStaph.ra
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    68c17eba60f6a35a59ac8c836f8d42f6a9b176a1 Thu Dec 20 13:55:09 2018 -0800
    add search on the gene track and the composite for the chains refs #19937
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    abcd7a8e9959d4bf0a88eb410aa93defaeb64b90 Thu Jan 3 13:11:32 2019 -0800
    chainNets have turned into two files refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/chainNetStaph0.ra
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    37d56bf57d47b9942917c75ff7ce1de71c56ff55 Sun Dec 30 15:37:03 2018 -0800
    chains renamed breakup into two parts and add frames to 369-way refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/chainNetStaph1.ra
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    37d56bf57d47b9942917c75ff7ce1de71c56ff55 Sun Dec 30 15:37:03 2018 -0800
    chains renamed breakup into two parts and add frames to 369-way refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/description.html
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    51a8e8e185abca43acab59e876c6a471a6781861 Wed Dec 19 22:35:13 2018 -0800
    add some extra description from NCBI records refs #19937
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    469a0e7e891caa6af3b08d15a9ee8f3f8ae2419b Thu Jan 3 13:41:05 2019 -0800
    add strain identifier refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.369way.ra
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    e170cdd68db4a72147a96a8a7a8cc4fc6bed28cb Sat Dec 29 12:20:34 2018 -0800
    first peek at 369-way alignment refs #19937
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    37d56bf57d47b9942917c75ff7ce1de71c56ff55 Sun Dec 30 15:37:03 2018 -0800
    chains renamed breakup into two parts and add frames to 369-way refs #19937
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    9b9004b5324785bedc73f6cf71d23c10c19b5867 Thu Jan 3 13:24:44 2019 -0800
    mafDot on for default refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra
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    02d6d5e6afdfca26ea2343fa551c7f247558cfa7 Thu Dec 20 13:55:15 2018 -0800
    add search on the gene track and the composite for the chains refs #19937
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    e170cdd68db4a72147a96a8a7a8cc4fc6bed28cb Sat Dec 29 12:20:34 2018 -0800
    first peek at 369-way alignment refs #19937
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    37d56bf57d47b9942917c75ff7ce1de71c56ff55 Sun Dec 30 15:37:03 2018 -0800
    chains renamed breakup into two parts and add frames to 369-way refs #19937
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    a686a883905d058d863c2b7b277f009864a6820c Mon Dec 31 00:59:19 2018 -0800
    adding composite track of AA profiles refs #19937
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    79a63f79023731177747e95e2fe8a75bbb152131 Mon Dec 31 18:38:24 2018 -0800
    rmsk default off and adjusting ordering of tracks in aaCounts refs #19937
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    c9c9d376cafa8d53bca01f3e96390748a0e34e8b Thu Jan 3 15:45:01 2019 -0800
    add the crispr 10K track refs #19937
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
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    63b37dcf81f1ed851ff43923826f00c94ee1c525 Thu Dec 20 09:11:06 2018 -0800
    adding description page for 77-way refs #22687
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    43446ffe54c2bc6edb87165e59a8f0fe1e5c4f58 Thu Dec 20 09:43:03 2018 -0800
    should be complete now refs #22687
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    c5acbfba184e067c55e10c1cef92cadf9f45d608 Thu Dec 20 09:46:44 2018 -0800
    correct Ensembl gene version refs #22687
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    0f1c23875281dce668f2ef56f3847f03da8be08d Fri Jan 4 10:21:02 2019 -0800
    add out links to the genomewiki tables refs #22687
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.77way.ra
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    14bffd2c4758a9164cc21109ca908ab9931eb197 Tue Dec 18 15:29:58 2018 -0800
    turning on frames refs #22687
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
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    0505afae76f4e9920c9282918ace35855714c866 Fri Dec 21 15:57:43 2018 -0800
    turn on crispr 10K track refs #21987
• src/hg/makeDb/trackDb/tagTypes.tab
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    4e4157d5f7c461907adad8c2ce06ab89dadb6d6b Sat Dec 29 12:21:04 2018 -0800
    first peek at staAur2 369-way alignment refs #19937
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    6162d6e72a3d8f462747598076f900166ca3d21e Mon Dec 31 11:55:03 2018 -0800
    allow bedNameLabel on bigBed refs #19937
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
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    8a34ff74a6ad743d9f2c7991d47e2d12c4ebade6 Tue Dec 18 13:42:27 2018 -0800
    correct 112 nematodes 22 flatworms refs #22599
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    c86362180325cce597de07f851950546caff9d02 Wed Dec 19 08:18:27 2018 -0800
    add note about phylogenetic tree generation refs #22599
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    560967fb8867514d348760a6d70cadb641488e4a Thu Dec 20 09:57:04 2018 -0800
    correcting comments refs #22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra
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    8a34ff74a6ad743d9f2c7991d47e2d12c4ebade6 Tue Dec 18 13:42:27 2018 -0800
    correct 112 nematodes 22 flatworms refs #22599
• src/hg/utils/automation/doBlastzChainNet.pl
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    a40a70471d623a9777faac53fbc39d1cbf11c35f Fri Dec 21 15:59:05 2018 -0800
    fix to tolerate non existent query database refs #19937
• src/hg/utils/automation/doCpgIslands.pl
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    adbe1dc27ea368dd35f6b1158c3a4c583d1f0d4a Thu Jan 3 14:49:47 2019 -0800
    eliminate /scratch/data/ cluster dependencies no longer present no redmine
• src/hg/utils/automation/doCrispr.pl
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    1969f496a39dcf1a66caec35800600f08dcff2f8 Fri Dec 21 16:03:33 2018 -0800
    more efficient construction of jobLists using the correct workhorse and now allow small cluster hub for some steps refs #21987
• src/hg/utils/automation/doGenscan.pl
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    adbe1dc27ea368dd35f6b1158c3a4c583d1f0d4a Thu Jan 3 14:49:47 2019 -0800
    eliminate /scratch/data/ cluster dependencies no longer present no redmine
• src/hg/utils/automation/doRecipBest.pl
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    a40a70471d623a9777faac53fbc39d1cbf11c35f Fri Dec 21 15:59:05 2018 -0800
    fix to tolerate non existent query database refs #19937
• src/hg/utils/automation/doRepeatMasker.pl
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    f36151f6f2352441aa81fecbc376a8bd78d20632 Fri Dec 21 16:01:36 2018 -0800
    new location for program on ku kluster no more /scratch/data/ available refs #19937
• src/hg/utils/automation/makeDownloads.pl
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    adbe1dc27ea368dd35f6b1158c3a4c583d1f0d4a Thu Jan 3 14:49:47 2019 -0800
    eliminate /scratch/data/ cluster dependencies no longer present no redmine
• src/hg/utils/automation/makePushQSql.pl
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    052576da94f31940e692de6e244968418fd31f06 Tue Dec 18 15:39:47 2018 -0800
    add the ncbiRefSeq files to the gbdb listings refs #22113
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/utils/phyloTrees/220way.nh
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    1967851cf7755877a221ade09aac480a7939aa13 Fri Dec 21 16:15:20 2018 -0800
    updating cotJap1 to cotJap2 refs #22687
• src/hg/utils/phyloTrees/asciiTree.pl
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    20094a79ca19c05188a331fa277552ece2da0a87 Fri Dec 21 16:14:42 2018 -0800
    need to take out all right parens) not just the first one refs #22687
• src/hg/utils/phyloTrees/binaryTree.pl
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    e99476a29297b7c4b01d7d71b6c256b407cd215a Sun Dec 23 14:55:16 2018 -0800
    correctly print out distances in floating point no scientific notation from TreeGraph2 refs #19937
• src/hg/utils/phyloTrees/commonNames.sh
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    07509b76c3ce5203539c9813c9403b0620261f6b Fri Dec 21 16:13:55 2018 -0800
    adding some updated assembly names refs #22687
• src/hg/utils/phyloTrees/vertebrates.txt
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    e47cec19ac058f45cd8c5b102895392b4e3c3bd4 Fri Dec 21 16:16:07 2018 -0800
    adding ambMex for Axoloti refs #21715
• src/htslib/vcf.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/inc/common.mk
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    630afe3b1e9cfddb738dadfd77bcde6b74c15dbf Sat Jan 5 16:20:18 2019 -0800
    using some static libraries on ubuntu with gcc-7 no redmine
• src/lib/dyOut.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/lib/maf.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    c35eeaeb4e0f0ae5434278fc3a6badde03264163 Mon Jan 7 10:15:59 2019 -0800
    v376 preview2, refs #22686
• src/utils/twoBitDup/twoBitDup.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine