All File Changes

v316_preview2 to v316_base (2015-05-04 to 2015-05-11) v316

• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 14, context: html, text, full: html, text
    Bugfix: when the trash file for user regions went away, the CGI was
    sending mixed signals to the view. For now, if the trash file goes
    away then prompt for regions if the user chooses defined regions.
    It would be better to have separate states for 'we have no regions
    and no previously typed regions' and 'we have no regions but do
    remember what you typed last time'.
    refs #14579
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 2, context: html, text, full: html, text
    changes to allow the mafSnp view to be selected on multiz tracks with
    snpTables #14970
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    fixing re-directing URL
    
  • lines changed 23, context: html, text, full: html, text
    Updated a pub entry, fixed some capitalization in titles to match our conventions elsewhere on page.
    
  • lines changed 1, context: html, text, full: html, text
    Updated this link to point to a published online source, per David. refs #15300.
    
  • lines changed 3, context: html, text, full: html, text
    Fixed some special characters that were not html-encoded and were displaying incorrectly as a result.
    
  • lines changed 8, context: html, text, full: html, text
    Fixed some links.
    
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    changes to allow the mafSnp view to be selected on multiz tracks with
    snpTables #14970
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v316
    
• src/hg/lib/grp.sql
  • lines changed 1, context: html, text, full: html, text
    drop grp table before attempting to create (no redmine)
    
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    Generate error rather than SEGV if genomeClade is not found (no redmine)
    
• src/hg/lib/hui.c
  • lines changed 9, context: html, text, full: html, text
    changes to allow the mafSnp view to be selected on multiz tracks with
    snpTables #14970
    
• src/hg/lib/mafGene.c
  • lines changed 1, context: html, text, full: html, text
    a few more changes to support snpView on tarSyr2 and hg38 20 ways #14970
    
• src/hg/makeDb/doc/hg38/multiz100way.txt
  • lines changed 1899, context: html, text, full: html, text
    have initial maf files refs #14560
    
  • lines changed 502, context: html, text, full: html, text
    loading frames and calculating 4D tree refs #14560
    
  • lines changed 498, context: html, text, full: html, text
    done with phastCons and phyloP refs #14560
    
• src/hg/makeDb/doc/hg38/snpView20way.txt
  • lines changed 28, context: html, text, full: html, text
    a few more changes to support snpView on tarSyr2 and hg38 20 ways #14970
    
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 16, context: html, text, full: html, text
    liftOver to micMur2 refs #15292
    
• src/hg/makeDb/doc/micMur2/initialBuild.txt
  • lines changed 452, context: html, text, full: html, text
    beginning build of browser refs #15292
    
  • lines changed 111, context: html, text, full: html, text
    running up genbank and last tracks refs #15292
    
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
  • lines changed 20, context: html, text, full: html, text
    a few more changes to support snpView on tarSyr2 and hg38 20 ways #14970
    
• src/hg/makeDb/doc/tarSyr2/snpView.txt
  • lines changed 28, context: html, text, full: html, text
    a few more changes to support snpView on tarSyr2 and hg38 20 ways #14970
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    Added micMur2; refs #15292
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    adding rules for micMur2 refs #15292
    
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    override matrix values for tarSyr2 refs #15112
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra
  • lines changed 1, context: html, text, full: html, text
    changes to allow the mafSnp view to be selected on multiz tracks with
    snpTables #14970
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 1, context: html, text, full: html, text
    changes to allow the mafSnp view to be selected on multiz tracks with
    snpTables #14970
    
• src/hg/makeDb/trackDb/human/hg38/alpha.7way.ra
  • lines changed 10, context: html, text, full: html, text
    better lables for these N-way tracks on alpha refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/betaPublic.7way.ra
  • lines changed 10, context: html, text, full: html, text
    better lables for these N-way tracks on alpha refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 536, context: html, text, full: html, text
    first peek at new 100-way refs #14560
    
  • lines changed 14, context: html, text, full: html, text
    updating to new assembly references from the hg19 set refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 3, context: html, text, full: html, text
    fixup dates and asterisk refs #14970
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 114, context: html, text, full: html, text
    first peek at new 100-way refs #14560
    
  • lines changed 1, context: html, text, full: html, text
    better lables for these N-way tracks on alpha refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra
  • lines changed 1, context: html, text, full: html, text
    better lables for these N-way tracks on alpha refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra
  • lines changed 1, context: html, text, full: html, text
    add snpTables to hg38 and tarSyr2 20ways #14970
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.7way.ra
  • lines changed 11, context: html, text, full: html, text
    better lables for these N-way tracks on alpha refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    add knownGeneOld8 refs #14639
    
  • lines changed 2, context: html, text, full: html, text
    first peek at new 100-way refs #14560
    
• src/hg/makeDb/trackDb/lancelet/braFlo1/description.html
  • lines changed 3, context: html, text, full: html, text
    Fixed special characters that weren't html-encoded and therefor were displaying incorrectly.
    
• src/hg/makeDb/trackDb/lancelet/braFlo2/description.html
  • lines changed 4, context: html, text, full: html, text
    Fixed special characters that weren't html-encoded and therefor were displaying incorrectly.
    
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link in photo credits.
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding micMur2 to the build refs #15292
    
• src/hg/makeDb/trackDb/mouseLemur/micMur2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding micMur2 to the build refs #15292
    
• src/hg/makeDb/trackDb/mouseLemur/micMur2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding micMur2 to the build refs #15292
    
• src/hg/makeDb/trackDb/mouseLemur/micMur2/gold.html
  • lines changed 33, context: html, text, full: html, text
    adding micMur2 to the build refs #15292
    
• src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding micMur2 to the build refs #15292
    
  • lines changed 5, context: html, text, full: html, text
    add search rule for gold table refs #15292
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    changes to allow the mafSnp view to be selected on multiz tracks with
    snpTables #14970
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.20way.ra
  • lines changed 1, context: html, text, full: html, text
    add Mm10 and CanFam3 to the chainNet ordering overrides refs #15112
    
  • lines changed 1, context: html, text, full: html, text
    add snpTables to hg38 and tarSyr2 20ways #14970
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.chainNet.ra
  • lines changed 12, context: html, text, full: html, text
    add Mm10 and CanFam3 to the chainNet ordering overrides refs #15112
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Changing colors for NCBI RefGene track, removing priority, refs #13673
    
• src/hg/makeDb/trackDb/treeShrew/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Adding matrix override for tarSyr2 chainNet track, refs #15112
    
• src/hg/utils/paSNP/makefile
  • lines changed 6, context: html, text, full: html, text
    paSNP, a little utility that parses output from mafGene to make the
    mafSnp table #14970
    
• src/hg/utils/paSNP/pa.c
  • lines changed 410, context: html, text, full: html, text
    paSNP, a little utility that parses output from mafGene to make the
    mafSnp table #14970
    
• src/hg/utils/paSNP/paSNP.c
  • lines changed 102, context: html, text, full: html, text
    paSNP, a little utility that parses output from mafGene to make the
    mafSnp table #14970
    
• src/utils/bedSmash/bedSmash.c
  • lines changed 67, context: html, text, full: html, text
    bedSmash utility used in building mafSnp track #14970
    
• src/utils/bedSmash/makefile
  • lines changed 3, context: html, text, full: html, text
    bedSmash utility used in building mafSnp track #14970
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v316 preview2 refs #15237
    
  • lines changed 3, context: html, text, full: html, text
    v316 final build refs #15288
    

• lines changed: 5140
• files changed: 61