All File Changes

v338_base to v339_preview (2016-09-06 to 2016-09-12) v339

• src/hg/cirm/cdw/cdwCleanMetaData/cdwCleanMetaData
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    4cf16e4f34294735825b05de85fbc3979e3d1f61 Wed Aug 24 11:16:15 2016 -0700
    fixing a small bug, refs #17918
    
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 4, context: html, text, full: html, text
    545cb32907ea074f7e0b236279866e215df81cca Mon Aug 15 10:38:28 2016 -0700
    Escaping in makeFileTags.
    
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    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
• src/hg/cirm/cdw/cdwMakeTrackViz/cdwMakeTrackViz.c
  • lines changed 1, context: html, text, full: html, text
    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
• src/hg/cirm/cdw/cdwReallyRemoveDataset/cdwReallyRemoveDataset.c
  • lines changed 67, context: html, text, full: html, text
    5439dc1e6afe1e4162e46a3a34ed9dfb9fbcd622 Wed Aug 31 11:06:18 2016 -0700
    Making a dataset removing utility.
    
• src/hg/cirm/cdw/cdwReallyRemoveDataset/makefile
  • lines changed 4, context: html, text, full: html, text
    5439dc1e6afe1e4162e46a3a34ed9dfb9fbcd622 Wed Aug 31 11:06:18 2016 -0700
    Making a dataset removing utility.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 1, context: html, text, full: html, text
    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 3, context: html, text, full: html, text
    419361576fff6aa0f3cd10f5bd76699dda59a4fa Sat Sep 10 11:10:51 2016 -0700
    Changing some hard paths to go off the CIRM environment variable so it works on pod and hgwdev.
    
• src/hg/cirm/cdw/cdwTextForIndex/cdwTextForIndex.c
  • lines changed 1, context: html, text, full: html, text
    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 4, context: html, text, full: html, text
    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
  • lines changed 54, context: html, text, full: html, text
    b3cf9e06b98c2a080bcebc6f0873cdeec639f4c6 Wed Sep 7 10:19:24 2016 -0700
    Fixing merge conflict with Chris, a very small one.
    
  • lines changed 2, context: html, text, full: html, text
    695de0d48c1a8502e2e3e3879fdf0b654441fd37 Wed Sep 7 10:48:42 2016 -0700
    Fixing typo in sample_label
    
  • lines changed 7, context: html, text, full: html, text
    76a352ba57f7b8e71048b644af6d4c47bf2c2f31 Wed Sep 7 12:09:16 2016 -0700
    removing a print statement that slipped past me, refs #17870
    
• src/hg/cirm/cdw/cdwWebBrowse/tagDescriptions.h
  • lines changed 2, context: html, text, full: html, text
    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 2, context: html, text, full: html, text
    5c772ecbcfd83c6420257bcf8b98fcdb8bd3b27e Wed Sep 7 10:14:27 2016 -0700
    Renaming body_part to sample_label.
    
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    5439dc1e6afe1e4162e46a3a34ed9dfb9fbcd622 Wed Aug 31 11:06:18 2016 -0700
    Making a dataset removing utility.
    
• src/hg/hgGene/gtex.c
  • lines changed 2, context: html, text, full: html, text
    f3987f39afa22e1099713ca3dfbfb3fe27987fa7 Thu Sep 8 11:36:46 2016 -0700
    Restore link to gene page of GTEx portal. It's working again.
    
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 8, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
  • lines changed 6, context: html, text, full: html, text
    6cbe864705942f1d802d552cbb8d09c7742015a0 Wed Sep 7 17:59:25 2016 -0700
    make sure bigGeneDataUrl support does maxItems support correctly
    
• src/hg/hgTracks/cds.c
  • lines changed 4, context: html, text, full: html, text
    e9aaeb801992b45089a21aa58b6f98a452eb4366 Wed Sep 7 13:38:00 2016 -0700
    don't grab DNA sequence in hgTracks if not going to be drawing codons or
    different bases.
    
  • lines changed 4, context: html, text, full: html, text
    04f62177f924e36ab071aa80e784d6f31fe1fd3b Wed Sep 7 15:32:23 2016 -0700
    oops...need to init DNA in a couple of other cases
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
  • lines changed 11, context: html, text, full: html, text
    6cbe864705942f1d802d552cbb8d09c7742015a0 Wed Sep 7 17:59:25 2016 -0700
    make sure bigGeneDataUrl support does maxItems support correctly
    
• src/hg/hgTracks/imageV2.c
  • lines changed 20, context: html, text, full: html, text
    f05bd698ed7a90ffc44565b5a8a4b128cbf05083 Thu Sep 8 16:14:07 2016 -0700
    optimization to avoid worrying about overlapping map boxes.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 99, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
  • lines changed 2, context: html, text, full: html, text
    6cbe864705942f1d802d552cbb8d09c7742015a0 Wed Sep 7 17:59:25 2016 -0700
    make sure bigGeneDataUrl support does maxItems support correctly
    
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/hgc/bigBedClick.c
  • lines changed 269, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/hgc/gtexClick.c
  • lines changed 2, context: html, text, full: html, text
    f3987f39afa22e1099713ca3dfbfb3fe27987fa7 Thu Sep 8 11:36:46 2016 -0700
    Restore link to gene page of GTEx portal. It's working again.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
  • lines changed 68, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
  • lines changed 3, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 10, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    e6a820eebfa703866fa83b6c8ba66e84289e15c7 Wed Aug 31 14:03:39 2016 -0700
    Correcting minor spelling mistake, no redmine
    
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    34fd3ea1e13f421b91a396ed9b9b1c4c2b8cbb6e Wed Sep 7 10:49:34 2016 -0700
    Fixing date on announcement per CR, refs #18038
    
• src/hg/htdocs/training/index.html
  • lines changed 28, context: html, text, full: html, text
    94dec759f9bc2b630836f5d097fa238f6f99cac7 Fri Sep 9 16:07:06 2016 -0700
    dropped ucsf workshop. added penn state and ashg
    
• src/hg/inc/genePred.h
  • lines changed 41, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/inc/jksql.h
  • lines changed 1, context: html, text, full: html, text
    ebf16fa660f3db7afb0e1fbaf3f02852c8e6587f Tue Sep 6 12:10:49 2016 -0700
    internal documention fixes
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/lib/estOrientInfo.c
  • lines changed 1, context: html, text, full: html, text
    ebf16fa660f3db7afb0e1fbaf3f02852c8e6587f Tue Sep 6 12:10:49 2016 -0700
    internal documention fixes
    
• src/hg/lib/genePred.c
  • lines changed 57, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/lib/hui.c
  • lines changed 11, context: html, text, full: html, text
    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    ebf16fa660f3db7afb0e1fbaf3f02852c8e6587f Tue Sep 6 12:10:49 2016 -0700
    internal documention fixes
    
• src/hg/makeDb/doc/gorGor5/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    bf6398e75cb1fed12a503a2b51f4c08fa9ffbf40 Wed Sep 7 14:28:47 2016 -0700
    correct Organism name at top of file refs #17580
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    77c3b05926fa9df961afec08d8205dda299e36ec Fri Sep 9 15:22:18 2016 -0700
    Matt found that the LRG tracks were missing one of the X/Y PAR mappings -- fixed script to handle multiple mappings. refs #13359
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 3, context: html, text, full: html, text
    77c3b05926fa9df961afec08d8205dda299e36ec Fri Sep 9 15:22:18 2016 -0700
    Matt found that the LRG tracks were missing one of the X/Y PAR mappings -- fixed script to handle multiple mappings. refs #13359
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 3, context: html, text, full: html, text
    a8c9fa3248e99b519a046e055db5fae64b348c4a Tue Sep 6 13:49:18 2016 -0700
    Updated DGV for hg38 (redumped because Matt found gene names were missing). refs #17351
    
• src/hg/makeDb/doc/ucscGenes/hg18.ucscGenes11.csh
  • lines changed 6, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 8, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
  • lines changed 7, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes16.csh
  • lines changed 8, context: html, text, full: html, text
    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
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    6fa996f377f2bf37bec542e3dbf1c758d9240bec Wed Sep 7 12:28:51 2016 -0700
    Rebuild of bioCyc pathways data for mm10 genes, this time for sure! refs #15315
    
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/genbank/src/copy/checkUpdate.sh
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/deleteLocks.sh
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
• src/hg/makeDb/genbank/src/copy/gbCopyDatabase
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/gbCopyMeta
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/gbCopyNew
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/gbValidate
  • lines changed 53, context: html, text, full: html, text
    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/gbdbRsync.sh
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
• src/hg/makeDb/genbank/src/copy/updateDb.sh
  • lines changed 25, context: html, text, full: html, text
    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
  • lines changed 103, context: html, text, full: html, text
    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/updateMeta.sh
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
  • lines changed 1, context: html, text, full: html, text
    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/copy/validateDb.sh
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
  • lines changed 53, context: html, text, full: html, text
    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/dbload/buildGrepIndex
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
• src/hg/makeDb/genbank/src/dbload/checkUpdate.sh
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/dbload/gbDbCopyMeta
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/dbload/gbDbLoadChanged
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    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/genbank/src/dbload/updateMetaDev.sh
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    e5d9d85922b152fe8165119f4571782a24893516 Wed Sep 7 10:19:46 2016 -0700
    checking in current state of Genbank scripts in anticipation of moving
    things around
    
  • lines changed 71, context: html, text, full: html, text
    f37eb3818b7be3f7d877a6b6769771703b12ad2d Wed Sep 7 10:32:43 2016 -0700
    moving around genbank update utilities
    
• src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
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    6ecb7a6a825de9746dfecf3f6094b4187a969ae5 Fri Sep 9 13:34:06 2016 -0700
    moving period outside of link, no redmine
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
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    67645c0b9245140af58ff6d11ec75820b3c43697 Wed Sep 7 16:03:34 2016 -0700
    oops.. maxItems snuck in trackDb for knownGene.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/trackDb/human/lrg.html
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    f234bb8bc20282b7b78483c3e68e86864f60f1fd Fri Sep 9 13:32:37 2016 -0700
    Rearranging sections on track description page. Fixing up references format, refs #13359
    
• src/hg/makeDb/trackDb/human/lrgTranscriptAli.html
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    f234bb8bc20282b7b78483c3e68e86864f60f1fd Fri Sep 9 13:32:37 2016 -0700
    Rearranging sections on track description page. Fixing up references format, refs #13359
    
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/makeDb/trackDb/tagTypes.tab
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/makeDb/trackDb/trackDb.ra
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    9045caeea248baaf8bc68a4410442558cfa0f407 Tue Sep 6 13:37:55 2016 -0700
    make knownGene use a maxItems of 1000000
    
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    67645c0b9245140af58ff6d11ec75820b3c43697 Wed Sep 7 16:03:34 2016 -0700
    oops.. maxItems snuck in trackDb for knownGene.
    
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/hg/utils/automation/parseLrgXml.pl
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    77c3b05926fa9df961afec08d8205dda299e36ec Fri Sep 9 15:22:18 2016 -0700
    Matt found that the LRG tracks were missing one of the X/Y PAR mappings -- fixed script to handle multiple mappings. refs #13359
    
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/hg/utils/genePredToBigGenePred/makeBigKnown
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    be8645fb43ba545dc342deb80cff297c5b677a5e Tue Sep 6 11:11:15 2016 -0700
    allow bigGenePred to be used to optimize knownGene on hgTracks #15259
    
• src/product/README.trackDb
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    a199e8112f2f392ea9ac8e98e88b389a3d58110a Wed Aug 31 16:41:13 2016 -0700
    fixing old doc which said cvs update directions now has git pull directions
    
• src/product/installer/browserSetup.sh
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    dd1510bdbd34d27b1a6d6c34d2212880943cb985 Tue Sep 6 14:15:13 2016 -0700
    trying to handle the big migration in the installer, refs #14399
    
• src/product/mirrorManual.txt
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    a199e8112f2f392ea9ac8e98e88b389a3d58110a Wed Aug 31 16:41:13 2016 -0700
    fixing old doc which said cvs update directions now has git pull directions
    
• src/utils/bedBetween
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/utils/bedOverlapMerge
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/utils/doCrispr.sh
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    
• src/utils/doLocusName
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
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• src/utils/makefile
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
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• src/utils/qa/weeklybld/buildEnv.csh
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    9308b7f978383665629d1731c41b98d9fd70125b Mon Sep 12 09:51:38 2016 -0700
    v339 preview1 refs #17934
    
• src/utils/tabRepl
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    c7723adc566681d4f69232076df356c36aa5a1cf Fri Sep 9 16:03:22 2016 -0700
    adding first versin of pipeline for crispr tracks and trackDb statements supporting external extra fields, refs #17235
    

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