File Changes for angie

v279_base to v280_preview (2013-02-12 to 2013-02-19) v280

• src/hg/altSplice/altSplice/makefile
  • lines changed 4, context: html, text, full: html, text
    Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
• src/hg/hgBlat/makefile
  • lines changed 2, context: html, text, full: html, text
    Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
• src/hg/hgKnownGeneList/makefile
  • lines changed 1, context: html, text, full: html, text
    Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 4, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 4, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/inc/gpFx.h
  • lines changed 5, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 66, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 3, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 47, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Track #9401 (DGV): Fixed a couple issues found by Brian L. (shortLabel, termRegex)
• src/inc/annoGrator.h
  • lines changed 24, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/inc/annoStreamer.h
  • lines changed 5, context: html, text, full: html, text
    Added setAutoSqlObject method to annoStreamer, to update both asObj andinternal state derived from it. (for #6152)
    
• src/lib/annoGrator.c
  • lines changed 41, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/lib/annoStreamer.c
  • lines changed 16, context: html, text, full: html, text
    Added setAutoSqlObject method to annoStreamer, to update both asObj andinternal state derived from it. (for #6152)