All File Changes

v331_preview to v331_preview2 (2016-03-28 to 2016-04-04) v331

• confs/preview.hg.conf
  • lines changed 238, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    Add support for filter on score. Show total median expression (from which score is computed) on details page. refs #15645
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 2, context: html, text, full: html, text
    Add support for filter on score. Show total median expression (from which score is computed) on details page. refs #15645
    
  • lines changed 36, context: html, text, full: html, text
    Add total expression to details page. Correct map box size problem. refs #15645
    
  • lines changed 21, context: html, text, full: html, text
    Added option to suppres display of gene model (instead just show a line covering gene extent). Kind of works, but theres a layout problem that causes bottom-most gene to be cut off
    
  • lines changed 4, context: html, text, full: html, text
    Strip off repetitive prefix from gene description. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Remove unhelpful indicator of up-regulation in mouseover. refs #15645
    
  • lines changed 31, context: html, text, full: html, text
    Add white background box to graph, and tweak graph sizes. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Darken graph outline box slightly. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Make magenta bar tip for exceeding view limits a touch bigger (JK input). refs #15645
    
  • lines changed 34, context: html, text, full: html, text
    Custom draw code for squish mode. refs #15645
    
  • lines changed 34, context: html, text, full: html, text
    Shenanigans to get squish mode working. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Another fix for compatibility with multi-region. refs #15645
    
  • lines changed 38, context: html, text, full: html, text
    Merge branch 'master' into gtexUiExon
    
  • lines changed 61, context: html, text, full: html, text
    Fixes to 'no gene model display', and make it default, as per JK. refs #15645
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 40, context: html, text, full: html, text
    Suppressing measureTiming track output averages when NOT in virtMode since these are redundant.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 9, context: html, text, full: html, text
    Add support for filter on score. Show total median expression (from which score is computed) on details page. refs #15645
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 17, context: html, text, full: html, text
    Add support for filter on score. Show total median expression (from which score is computed) on details page. refs #15645
    
  • lines changed 47, context: html, text, full: html, text
    Fixes #17096. Enhanced nextExon hover labels explains what it does now.
    
  • lines changed 6, context: html, text, full: html, text
    Fixes gtex track by accounting for label width.
    
  • lines changed 2, context: html, text, full: html, text
    Finally found where labeling happens, updating comment
    
  • lines changed 17, context: html, text, full: html, text
    I re-worked this so it would be more correct for gtex pack labels.
    
  • lines changed 1, context: html, text, full: html, text
    oops. pack leftLabelSize adjustment fixed.
    
• src/hg/hgc/gtexClick.c
  • lines changed 9, context: html, text, full: html, text
    Add total expression to details page. Correct map box size problem. refs #15645
    
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    snp125's getGPsWithFrames assumed that if a genePred table has an exonFrames column
    then that column contains frames. However, hg19's GENCODE Basic V19 has an empty
    exonFrames column, which caused a SEGV downstream when trying to predict a coding SNP's
    effect on a gene. So, check for null exonFrames and compute if necessary.
    refs #16777 (note 36)
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 23, context: html, text, full: html, text
    announcing new video. refs #17102
    
  • lines changed 24407, context: html, text, full: html, text
    trying to fix merge conflict
    
• src/hg/htdocs/images/training/vidTitle08.jpg
  • lines changed 0, context: html, text, full: html, text
    releasing new video
    
• src/hg/htdocs/indexNews.bak.html
  • lines changed 221, context: html, text, full: html, text
    trying to fix merge conflict
    
• src/hg/htdocs/indexNews.html
  • lines changed 50, context: html, text, full: html, text
    4/1 joke!
    
  • lines changed 41, context: html, text, full: html, text
    announcing new video. refs #17102
    
  • lines changed 421, context: html, text, full: html, text
    trying to fix merge conflict
    
• src/hg/htdocs/training/index.html
  • lines changed 19, context: html, text, full: html, text
    removing completed CSUMB, adding two Denmark workshops
    
  • lines changed 296, context: html, text, full: html, text
    trying to fix merge conflict
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 57, context: html, text, full: html, text
    releasing new video
    
  • lines changed 708, context: html, text, full: html, text
    trying to fix merge conflict
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 4, context: html, text, full: html, text
    Add support for filter on score. Show total median expression (from which score is computed) on details page. refs #15645
    
• src/hg/inc/gtexUi.h
  • lines changed 4, context: html, text, full: html, text
    Added option to suppres display of gene model (instead just show a line covering gene extent). Kind of works, but theres a layout problem that causes bottom-most gene to be cut off
    
  • lines changed 1, context: html, text, full: html, text
    Fixes to 'no gene model display', and make it default, as per JK. refs #15645
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 10, context: html, text, full: html, text
    Add support for filter on score. Show total median expression (from which score is computed) on details page. refs #15645
    
• src/hg/lib/gtexUi.c
  • lines changed 25, context: html, text, full: html, text
    Added option to suppres display of gene model (instead just show a line covering gene extent). Kind of works, but theres a layout problem that causes bottom-most gene to be cut off
    
  • lines changed 18, context: html, text, full: html, text
    Hide M/F comparison feature for now. Need to rethink values displayed in comparison (should be fold or else indicate total expression). refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Merge master, fix conflict.
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
  • lines changed 897, context: html, text, full: html, text
    start UCSC genes for hg38 based on Gencode V24
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Adding rheMac8 beta genbank updates, refs #16744
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Add gtexDonor table. refs #15645
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Removing release tags ahead of lens patent track release, refs #14486
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 4, context: html, text, full: html, text
    Tweak title and add release tags.
    
  • lines changed 1, context: html, text, full: html, text
    Remove offending release tag from composite.
    
  • lines changed 1, context: html, text, full: html, text
    Tweak track label. Simpler is better. refs #15645
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    testing a snpedia track
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Removing release tags ahead of lens patent track release, refs #14486
    
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    refs #14486: fixing invalid mouse link and changing boundaries
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Removing release tags ahead of lens patent track release, refs #14486
    
  • lines changed 1, context: html, text, full: html, text
    refs #14486: fixing invalid mouse link and changing boundaries
    
• src/lib/tests/testSum.c
  • lines changed 35, context: html, text, full: html, text
    Fix test build err
    
• src/lib/tests/testSumDoubles.c
  • lines changed 35, context: html, text, full: html, text
    Fix test build err
    
• src/utils/qa/runJoiner.csh
  • lines changed 1, context: html, text, full: html, text
    added tablename to output when not in tablesIgnored, per cath
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 4, context: html, text, full: html, text
    v331 preview2 refs #17072
    

• lines changed: 27987
• files changed: 59