File Changes for hiram

v336_preview to v336_preview2 (2016-07-11 to 2016-07-18) v336

• src/hg/bedIntersect/tests/input/chrUn_LVXT01056135v1.bed
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    ccc04f192749cdcc1e834acf9598d052e5b6783d Wed Jul 13 15:46:35 2016 -0700
    added commutativeTest target refs #17704
    
• src/hg/bedIntersect/tests/input/chrUn_LVXT01056135v1Gaps.bed
  • lines changed 8, context: html, text, full: html, text
    ccc04f192749cdcc1e834acf9598d052e5b6783d Wed Jul 13 15:46:35 2016 -0700
    added commutativeTest target refs #17704
    
• src/hg/bedIntersect/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    ccc04f192749cdcc1e834acf9598d052e5b6783d Wed Jul 13 15:46:35 2016 -0700
    added commutativeTest target refs #17704
    
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    4512514645d6913d3c7f5138865365a4a6cb3c2a Wed Jul 13 17:17:54 2016 -0700
    just need better minCoverage, not a bug refs #17704
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    42d324f8c666f5f7188c4ef8ca97c78140f9a595 Fri Jul 15 15:20:42 2016 -0700
    try displaying refSeqAli table as a PSL track in refSeqComposite refs #13673
    
• src/hg/trfBig/trfBig.c
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    6d3019aadc40b26d64a8e3191fca8084a8055d67 Thu Jul 14 11:31:31 2016 -0700
    correct option processing for new trf v4.09 options refs #17580
    
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 332, context: html, text, full: html, text
    a66173eb20d03bf8e03b78321a6ac42ab4a4fc36 Thu Jul 14 13:16:25 2016 -0700
    constructing description.html gateway page and repeat masker bigBed files and index table for all assemblies in collection refs #13553
    
• src/hg/utils/automation/asmHubHtml.pl
  • lines changed 112, context: html, text, full: html, text
    a66173eb20d03bf8e03b78321a6ac42ab4a4fc36 Thu Jul 14 13:16:25 2016 -0700
    constructing description.html gateway page and repeat masker bigBed files and index table for all assemblies in collection refs #13553
    
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 98, context: html, text, full: html, text
    a66173eb20d03bf8e03b78321a6ac42ab4a4fc36 Thu Jul 14 13:16:25 2016 -0700
    constructing description.html gateway page and repeat masker bigBed files and index table for all assemblies in collection refs #13553
    
• src/hg/utils/automation/asmHubTrackDb.sh
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    9dcd25d3b353e416897abb26876daaa5fe1c6c51 Tue Jul 12 13:55:54 2016 -0700
    this is constructing a minimal assembly hub with assembly gap gc5Base trackes refs #13553
    
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    0b6dc28cf48e06936e3a56bb2cad7dc3108b2b91 Fri Jul 15 09:16:33 2016 -0700
    complete repeatMasker and added simpleRepeats refs #13553
    
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    428d5d7480823b3ccc841dda9a11015f3bb836f0 Sat Jul 16 14:29:24 2016 -0700
    trying out a gene track refs #13553
    
• src/hg/utils/automation/doAssemblyHub.pl
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    cfd17588c27dd46bca6f9f49b5f6f8516ff09f30 Mon Jul 11 11:08:17 2016 -0700
    fixup some broken code refs #13553
    
  • lines changed 106, context: html, text, full: html, text
    8d7025736ec2243773904369142c5a4233d83ab4 Mon Jul 11 14:48:23 2016 -0700
    assembly gap gc5Base and gatewayPage.html working refs #13553
    
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    729090c69502053bffc361ec44830fee22a97fe9 Tue Jul 12 13:56:00 2016 -0700
    this is constructing a minimal assembly hub with assembly gap gc5Base trackes refs #13553
    
  • lines changed 39, context: html, text, full: html, text
    a6cea0fbd88d7a83fdb3585d9ac010a8b98e9dc3 Thu Jul 14 13:12:57 2016 -0700
    added repeatMasker step refs #13553
    
  • lines changed 48, context: html, text, full: html, text
    042c30bf42780cc2fd3cf6a8e1f3bb452820d5a7 Fri Jul 15 09:13:18 2016 -0700
    now running simpleRepeats refs #13553
    
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    c10461bdc16c89b939a01f5389134b10869434df Fri Jul 15 14:32:13 2016 -0700
    running up allGaps data refs #13553
    
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    293f3895afcb62515ae62c6383e8c9607ef4a16a Fri Jul 15 14:58:50 2016 -0700
    running up the idKeys data for lifting reference refs #13553
    
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    ac6b56c4f50c0a47fe98ddf3f488c99f33532f3a Sat Jul 16 18:42:02 2016 -0700
    add the addMask step to add together the repeatMasker and simpleRepeat results for a masked 2bit file refs #13553
    
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 18, context: html, text, full: html, text
    8674ad6258c79ff4e04f46553a2631ec8cfe7501 Thu Jul 14 11:33:31 2016 -0700
    correct processing tmp directory for assembly hub build refs #13553
    
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 26, context: html, text, full: html, text
    589373cd4495395746e0ddcae562aa483835586c Thu Jul 14 11:33:05 2016 -0700
    correct processing tmp directory for assembly hub build refs #13553
    
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    70120cf951e38933e4f19fe774fd9fd9bf98b11a Thu Jul 14 20:54:10 2016 -0700
    creating bigBed during doFilter refs #13553
    
• src/product/scripts/fetchMinimalGbdb.sh
  • lines changed 1, context: html, text, full: html, text
    888a33b88aa0a243dfce9ca459a97d8bc9d5e760 Tue Jul 12 11:29:01 2016 -0700
    eliminate warning messages when no nib directory refs #17676
    
• src/utils/bedInvert.pl
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    9b4e3092e23d37d97634b3f09002bec996bd633e Thu Jul 14 16:21:14 2016 -0700
    bed inversion, show gaps between elements refs #13553
    
• src/utils/qa/weeklybld/buildEnv.csh
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    d096495c88c94d8f1da8b9aba04203b99ffd87f4 Mon Jul 18 11:14:29 2016 -0700
    v336 preview2