Commits for angie

v315_base to v316_preview (2015-04-20 to 2015-04-27) v316

• Loaded 1000 Genomes Phase 3 variants and accessible regions & added to trackDb.
  Still need to write descriptions.
  refs #14325
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 33, context: html, text, full: html, text
• cleanup: variable renaming, getting rid of unnecessary second conn,
  use bigDataUrl if it's present regardless of hub/db, use existing
  lib function instead of ad-hoc copy-paste.
  
  • src/hg/lib/hAnno.c - lines changed 30, context: html, text, full: html, text
• Moved hgVai's and hgIntegrator's duplicated NO_MAX_ROWS to hAnno.h as ANNO_NO_LIMIT.
  
  • src/hg/hgIntegrator/hgIntegrator.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgVai/hgVai.c - lines changed 10, context: html, text, full: html, text
  • src/hg/inc/hAnno.h - lines changed 4, context: html, text, full: html, text
• In getBedFieldSlNameList, when parsing the field string from bedSqlFieldsExceptForChrom,
  skip over placeholder field '.' in addition to placeholder 0. Letting the '.' slip through
  was not a problem until 1d8a8611 in which joinerDtfFromDottedTriple was changed to use
  strrchr instead of strchr to separate the field name from the track name, to accommodate
  track hubs with . in the track name.
  refs #15117
  
  • src/hg/hgTables/joining.c - lines changed 2, context: html, text, full: html, text
• Apply some band-aids to fix broken filterFields for bigDataUrl-only bigBed tracks.
  There are still way too many places in hgTables code that use isXyzTable(table, conn)
  even when tdb is available. I think all those places need to be fixed to pass in
  tdb if they have it, or NULL if they don't. The type-testers should use tdb if
  possible, and fall back to using table & conn if tdb is NULL.
  refs #14379, #15059
  
  • src/hg/hgTables/bigBed.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 6, context: html, text, full: html, text
• Adding .gitattributes files in directories that contain only compiled JS
  that is not going to be hand-edited, only replaced with newly compiled JS.
  
  • src/hg/js/external/.gitattributes - lines changed 1, context: html, text, full: html, text
• Fixing some style inconsistencies that Matt noted.
  refs #14579
  
  • src/hg/htdocs/style/HGStyle.css - lines changed 27, context: html, text, full: html, text
  • src/hg/js/react/hgIntegrator/hgIntegrator.jsx - lines changed 7, context: html, text, full: html, text
  • src/hg/js/react/lib/Section.jsx - lines changed 1, context: html, text, full: html, text