Commits for angie

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

• Added Missense-only VCF tracks from Gire et al.
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/automation/gireVcfToUcsc.pl - lines changed 51, context: html, text, full: html, text
• It's 101 not 102.
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
  
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014SpecificSnps.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 29, context: html, text, full: html, text
• Extracted an nh-like tree from Gire et al. supplemental materials.
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 12, 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/htdocs/ebolaPortal/index.html - lines changed 21, context: html, text, full: html, text
• Added Intra-host variants from Gire et al.
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra - 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.
  
  • src/lib/hacTree.c - lines changed 7, context: html, text, full: html, text
• Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014FixedMissense.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra - lines changed 8, context: html, text, full: html, text
• Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 122, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014KikwitMissense.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014MayingaMissense.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014PolymorphicMissense.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra - lines changed 30, context: html, text, full: html, text
• The Kikit and Mayinga diff tracks are only for the GP gene; make that clear in shortLabel.
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra - lines changed 2, 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/doc/eboVir3/gire.txt - lines changed 331, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014FixedMissense.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014KikwitMissense.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014MayingaMissense.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014PolymorphicMissense.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gire2014SpecificSnps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gireZebov.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gire2014FixedMissense.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gire2014KikwitMissense.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gire2014MayingaMissense.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gire2014PolymorphicMissense.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gire2014SpecificSnps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gireZebov.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/trackDb.gire.ra - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/trackDb.ra - lines changed 1, 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/hgTracks/vcfTrack.c - lines changed 4, context: html, text, full: html, text
• Adding include-files for Methods and References sections of Gire et al. tracks.
  • src/hg/makeDb/trackDb/ebola/gireMethods.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gireReferences.html - lines changed 21, context: html, text, full: html, text