File Changes for angie

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

• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 5, 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/hgTables/bigBed.c
  • lines changed 6, 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/filterFields.c
  • lines changed 10, 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/hgTables.h
  • lines changed 1, 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/joining.c
  • lines changed 2, 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/hgVai/hgVai.c
  • lines changed 10, 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/htdocs/style/HGStyle.css
  • lines changed 27, context: html, text, full: html, text
    Fixing some style inconsistencies that Matt noted.
    refs #14579
    
• src/hg/inc/hAnno.h
  • lines changed 4, 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/inc/trackDb.h
  • lines changed 6, 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/js/external/.gitattributes
  • lines changed 1, 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/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 7, context: html, text, full: html, text
    Fixing some style inconsistencies that Matt noted.
    refs #14579
    
• src/hg/js/react/lib/Section.jsx
  • lines changed 1, context: html, text, full: html, text
    Fixing some style inconsistencies that Matt noted.
    refs #14579
    
• src/hg/lib/hAnno.c
  • lines changed 30, 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/makeDb/doc/hg19.txt
  • lines changed 62, context: html, text, full: html, text
    Loaded 1000 Genomes Phase 3 variants and accessible regions & added to trackDb.
    Still need to write descriptions.
    refs #14325
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 33, context: html, text, full: html, text
    Loaded 1000 Genomes Phase 3 variants and accessible regions & added to trackDb.
    Still need to write descriptions.
    refs #14325