File Changes for angie

v282_base to v283_preview (2013-04-16 to 2013-04-23) v283

• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 22, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 44, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/inc/annoGrateWigDb.h
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 2, context: html, text, full: html, text
    Patching up one more mem leak for #6152.
• src/hg/inc/annoStreamDb.h
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/hg/inc/annoStreamWig.h
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/hg/inc/genePred.h
  • lines changed 2, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/lib/annoFormatVep.c
  • lines changed 50, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 27, context: html, text, full: html, text
    Patching up one more mem leak for #6152.
  • lines changed 6, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
  • lines changed 17, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/lib/annoGrateWigDb.c
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 17, context: html, text, full: html, text
    Patching up one more mem leak for #6152.
  • lines changed 3, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
  • lines changed 5, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/lib/annoStreamDb.c
  • lines changed 4, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 6, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/hg/lib/annoStreamWig.c
  • lines changed 13, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 7, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/hg/lib/genePred.c
  • lines changed 22, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 79, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 7, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 1, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/inc/annoAssembly.h
  • lines changed 24, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoColumn.h
  • lines changed 26, context: html, text, full: html, text
    Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
• src/inc/annoFormatter.h
  • lines changed 19, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoGrateWig.h
  • lines changed 1, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoGrator.h
  • lines changed 3, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoGratorQuery.h
  • lines changed 19, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoRow.h
  • lines changed 1, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/inc/annoStreamBigBed.h
  • lines changed 1, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoStreamBigWig.h
  • lines changed 1, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoStreamTab.h
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoStreamVcf.h
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/inc/annoStreamer.h
  • lines changed 28, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 12, context: html, text, full: html, text
    Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
  • lines changed 2, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/inc/asParse.h
  • lines changed 14, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/lib/annoAssembly.c
  • lines changed 33, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/lib/annoColumn.c
  • lines changed 41, context: html, text, full: html, text
    Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
• src/lib/annoFormatTab.c
  • lines changed 22, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 9, context: html, text, full: html, text
    Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
  • lines changed 2, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
  • lines changed 1, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/lib/annoFormatter.c
  • lines changed 13, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/lib/annoGrateWig.c
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 2, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/lib/annoGrator.c
  • lines changed 10, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 20, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/lib/annoGratorQuery.c
  • lines changed 81, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
• src/lib/annoRow.c
  • lines changed 1, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/lib/annoStreamBigBed.c
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 3, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/lib/annoStreamBigWig.c
  • lines changed 2, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 8, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/lib/annoStreamTab.c
  • lines changed 3, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 1, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/lib/annoStreamVcf.c
  • lines changed 3, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 5, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
  • lines changed 1, context: html, text, full: html, text
    Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
    
• src/lib/annoStreamer.c
  • lines changed 10, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 18, context: html, text, full: html, text
    Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
  • lines changed 5, context: html, text, full: html, text
    Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
    explicitly pass streamers(/grators) along with the rows that they
    produced into formatters. ref #6152
    
  • lines changed 1, context: html, text, full: html, text
    Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152