File Changes for angie

v306_preview2 to v306_base (2014-09-15 to 2014-09-22) v306

• src/hg/hgTracks/vcfTrack.c
  • lines changed 4, context: html, text, full: html, text
    Use vcfGenotype's isHaploid field instead of comparing chrom to chrY (that was messing up display of ebola which is haploid).
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 21, context: html, text, full: html, text
    Reformatted the Scientific Links section to include article titles(linked to PubMed) following each article's summary, and PDF links
    to full PDF at journals. Corrected some spelling errors.
    Removed hostname, position and hgsid from links to browser.
    
• src/hg/makeDb/doc/eboVir2/gire.txt
  • lines changed 67, context: html, text, full: html, text
    Added Missense-only VCF tracks from Gire et al.
  • lines changed 77, context: html, text, full: html, text
    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 12, context: html, text, full: html, text
    Extracted an nh-like tree from Gire et al. supplemental materials.
  • lines changed 24, context: html, text, full: html, text
    Added Intra-host variants from Gire et al.
  • lines changed 51, context: html, text, full: html, text
    Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
  • lines changed 122, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
• src/hg/makeDb/doc/eboVir3/gire.txt
  • lines changed 331, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014FixedMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014KikwitMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014MayingaMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014PolymorphicMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014SpecificSnps.html
  • lines changed 23, context: html, text, full: html, text
    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 28, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gireZebov.html
  • lines changed 16, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra
  • lines changed 35, context: html, text, full: html, text
    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 7, context: html, text, full: html, text
    Added Intra-host variants from Gire et al.
  • lines changed 8, context: html, text, full: html, text
    Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
  • lines changed 30, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 2, context: html, text, full: html, text
    The Kikit and Mayinga diff tracks are only for the GP gene; make that clear in shortLabel.
  • lines changed 78, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Added Missense-only VCF tracks from Gire et al.
  • lines changed 1, context: html, text, full: html, text
    It's 101 not 102.
  • lines changed 29, context: html, text, full: html, text
    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 1, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gire2014FixedMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gire2014KikwitMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gire2014MayingaMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gire2014PolymorphicMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gire2014SpecificSnps.html
  • lines changed 28, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gireMethods.html
  • lines changed 21, context: html, text, full: html, text
    Adding include-files for Methods and References sections of Gire et al. tracks.
• src/hg/makeDb/trackDb/ebola/gireReferences.html
  • lines changed 21, context: html, text, full: html, text
    Adding include-files for Methods and References sections of Gire et al. tracks.
• src/hg/makeDb/trackDb/ebola/gireZebov.html
  • lines changed 16, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/trackDb.gire.ra
  • lines changed 89, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/utils/automation/gireVcfToUcsc.pl
  • lines changed 51, context: html, text, full: html, text
    Added Missense-only VCF tracks from Gire et al.
• src/lib/hacTree.c
  • lines changed 7, context: html, text, full: html, text
    Missing NULL check that somehow hid for a long time, then reared itsugly head when zoomed in to a small region in eboVir2.
    I should really just switch vcfTrack over to using Jim's improved
    hacTree, when the ebola dust settles.