File Changes for braney

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

• 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
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    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/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
    
• 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/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/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/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
    
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.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/genbank/src/copy/checkUpdate.sh
  • lines changed 15, 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/deleteLocks.sh
  • lines changed 11, 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
    
• src/hg/makeDb/genbank/src/copy/gbCopyDatabase
  • 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/gbCopyMeta
  • 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/gbCopyNew
  • lines changed 15, 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/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
  • lines changed 2, 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
    
• 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
  • lines changed 1, 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 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
  • lines changed 53, 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 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
  • lines changed 1, 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
    
• src/hg/makeDb/genbank/src/dbload/checkUpdate.sh
  • lines changed 8, 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 22, 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/gbDbCopyMeta
  • 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/genbank/src/dbload/gbDbLoadChanged
  • lines changed 22, 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/updateMetaDev.sh
  • lines changed 2, 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 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
  • 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/makeDb/trackDb/human/hg19/trackDb.ra
  • 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/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 39, 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/trackDb/human/hg38/knownGene.ra
  • 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 1, context: html, text, full: html, text
    67645c0b9245140af58ff6d11ec75820b3c43697 Wed Sep 7 16:03:34 2016 -0700
    oops.. maxItems snuck in trackDb for knownGene.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • 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/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • 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/makeDb/trackDb/mouse/mm9/defaultPriority.ra
  • 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/makeDb/trackDb/tagTypes.tab
  • 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/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9045caeea248baaf8bc68a4410442558cfa0f407 Tue Sep 6 13:37:55 2016 -0700
    make knownGene use a maxItems of 1000000
    
  • lines changed 1, context: html, text, full: html, text
    67645c0b9245140af58ff6d11ec75820b3c43697 Wed Sep 7 16:03:34 2016 -0700
    oops.. maxItems snuck in trackDb for knownGene.
    
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 107, 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/utils/genePredToBigGenePred/makeBigKnown
  • lines changed 14, 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