All File Changes

v318_preview2 to v318_base (2015-06-15 to 2015-06-22) v318

• src/hg/hgMenubar/hgMenubar
  • lines changed 104, context: html, text, full: html, text
    Cleanup commits for hgMenubar
    
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 65, context: html, text, full: html, text
    Replaced perl CGI with C CGI for writing static page menu bars
    
• src/hg/hgMenubar/makefile
  • lines changed 24, context: html, text, full: html, text
    Cleanup commits for hgMenubar
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    let users show GENCODE transcript id in UCSC genes refs #14639
    
  • lines changed 2, context: html, text, full: html, text
    fix typo "show composite" to "show comprehensive" refs #14639
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 13, context: html, text, full: html, text
    let users show GENCODE transcript id in UCSC genes refs #14639
    
  • lines changed 3, context: html, text, full: html, text
    fix typo "show composite" to "show comprehensive" refs #14639
    
• src/hg/htdocs/goldenPath/help/chimera.html
  • lines changed 3, context: html, text, full: html, text
    Slightly adjusting menubar include in prep for scripted replacement with CGI menubar
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 3, context: html, text, full: html, text
    Reverting to old colors until next release, refs #15389
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v318
    
• src/hg/lib/bedDetail.c
  • lines changed 3, context: html, text, full: html, text
    Fixing bad bed detail .as description, refs #15567
    
• src/hg/makeDb/doc/danRer10/ncbiGene.txt
  • lines changed 20, context: html, text, full: html, text
    latest build doc for ncbi refSeq #13673
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 21, context: html, text, full: html, text
    Added entry for GWIPS-viz Ribo-seq track; refs #14066
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 29, context: html, text, full: html, text
    update score column on the cloneEnd tables refs #13713
    
• src/hg/makeDb/doc/hg38/ncbiGene.txt
  • lines changed 55, context: html, text, full: html, text
    latest build doc for ncbi refSeq #13673
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 1, context: html, text, full: html, text
    Add source table for clusters to all.joiner. regs #14733
    
  • lines changed 68, context: html, text, full: html, text
    Cleanup signalvalue and pvalues in hotspot and peaks. Also, make sure gbdb points to scored hotspots (QA issue). refs #14733
    
• src/hg/makeDb/doc/hg38/stsMap.txt
  • lines changed 524, context: html, text, full: html, text
    begin alignment of STS markers to hg38 refs #15524
    
• src/hg/makeDb/doc/manPen1/initialBuild.txt
  • lines changed 538, context: html, text, full: html, text
    ready for downloads refs #15515
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 22, context: html, text, full: html, text
    latest build doc for ncbi refSeq #13673
    
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 31, context: html, text, full: html, text
    add gold/assembly track search rule refs #8231
    
  • lines changed 11, context: html, text, full: html, text
    add augustus gene construction process refs #13088
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 22, context: html, text, full: html, text
    latest build doc for ncbi refSeq #13673
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ce11 - C. elegans WS245 refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    Added manPen1 - Pangolin/Manis pentadactyla (javanica)refs #15515
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    Added ce11 - C. elegans WS245 refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    Added manPen1 - Pangolin/Manis pentadactyla (javanica)refs #15515
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Add source table for clusters to all.joiner. regs #14733
    
  • lines changed 1, context: html, text, full: html, text
    Added gwipsvizRiboseq to hg19 tablesIgnored; refs #14066
    
  • lines changed 11, context: html, text, full: html, text
    Added manPen1 - Chinese Pangolin/Manis pentadactyl arefs #15515
    
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    adding search rule for gold/assembly table refs #8231
    
• src/hg/makeDb/trackDb/gwipsvizRiboseq.html
  • lines changed 4, context: html, text, full: html, text
    Italicized 'et al' in in-text citations; refs #14066
    
  • lines changed 2, context: html, text, full: html, text
    Added sentence describing what the values on the y-axis represent; refs #14066
    
  • lines changed 9, context: html, text, full: html, text
    Moved and slightly edited sentence about y-axis values; refs #14066
    
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
  • lines changed 39, context: html, text, full: html, text
    grouping tracks for better visibility control refs #13713
    
• src/hg/makeDb/trackDb/human/cloneEndSuper.html
  • lines changed 44, context: html, text, full: html, text
    adding information from previous BAC Ends track refs #13713
    
  • lines changed 41, context: html, text, full: html, text
    cleaning up the comments from the bacEnd track description refs #13713
    
  • lines changed 22, context: html, text, full: html, text
    adding links from library name to NCBI clone library information refs #13713
    
  • lines changed 6, context: html, text, full: html, text
    add the counts of dropped ends and multiple mappings to the table refs #13713
    
  • lines changed 1, context: html, text, full: html, text
    grammer correction refs #13713
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
  • lines changed 14, context: html, text, full: html, text
    Update supertrack description as oer QA comments. refs #14733
    
  • lines changed 1, context: html, text, full: html, text
    Round 2 of edits to the ENCODE Regulation track description pages; refs #14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
  • lines changed 20, context: html, text, full: html, text
    Round 2 of edits to the ENCODE Regulation track description pages; refs #14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseSignal.html
  • lines changed 8, context: html, text, full: html, text
    Round 2 of edits to the ENCODE Regulation track description pages; refs #14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k27ac.html
  • lines changed 1, context: html, text, full: html, text
    Corrected 'acylation' to 'acetylation'; refs #14568
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k4me1.html
  • lines changed 1, context: html, text, full: html, text
    Corrected 'acylation' to 'acetylation'; refs #14568
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k4me3.html
  • lines changed 1, context: html, text, full: html, text
    Corrected 'acylation' to 'acetylation'; refs #14568
    
• src/hg/makeDb/trackDb/human/hgmd.html
  • lines changed 10, context: html, text, full: html, text
    refs #15555, updating lovd and hgmd track docs
    
• src/hg/makeDb/trackDb/human/lovd.html
  • lines changed 3, context: html, text, full: html, text
    refs #15555, updating lovd and hgmd track docs
    
  • lines changed 17, context: html, text, full: html, text
    refs #15555, adding lovd exception list so users know what is missing
    
  • lines changed 2, context: html, text, full: html, text
    refs #15555, add missing link to LOVD FAQ
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Changed default track settings for GWIPS-viz Ribo-seq; refs #14066
    
  • lines changed 1, context: html, text, full: html, text
    Added viewLimitsMax entry to GWIPS-viz Ribo-seq track; refs #14066
    
  • lines changed 1, context: html, text, full: html, text
    Removed viewLimitsMax setting - not supported for bigWigs; refs #14066
    
  • lines changed 1, context: html, text, full: html, text
    Adding data range to gwips riboseq track, refs #14066
    
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding hgMenubar to the hg/ makefile
    
• src/hg/stsMarkers/headchg
  • lines changed 6, context: html, text, full: html, text
    better to use /usr/bin/env perl instead of /usr/local/bin/perl refs #15524
    
• src/hg/stsMarkers/sorttbl
  • lines changed 5, context: html, text, full: html, text
    better to use /usr/bin/env perl instead of /usr/local/bin/perl refs #15524
    
• src/hg/stsMarkers/uniqtbl
  • lines changed 6, context: html, text, full: html, text
    better to use /usr/bin/env perl instead of /usr/local/bin/perl refs #15524
    
• src/inc/filePath.h
  • lines changed 3, context: html, text, full: html, text
    Adding a function to generate relative URLs
    
• src/lib/filePath.c
  • lines changed 41, context: html, text, full: html, text
    Adding a function to generate relative URLs
    
• src/lib/vcf.c
  • lines changed 2, context: html, text, full: html, text
    Don't refuse VCF v4.2 files -- display as well as we can. At some point,
    someone should take a closer look at the 4.2 spec to see what changes will
    require code changes.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v318 final build refs #15560
    

• lines changed: 1911
• files changed: 63