File Changes for angie

v265_preview2 to v265_base (2012-03-20 to 2012-03-27) v265

• src/hg/hgTracks/gvfTrack.c
  • lines changed 8, context: html, text, full: html, text
    Track #7090 (ISCA update): Adding abbreviations for several morevariant origin terms from John Lopez (NCBI).
• src/hg/inc/annoStreamDb.h
  • lines changed 14, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/inc/jksql.h
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/annoStreamDb.c
  • lines changed 187, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 117, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 22, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/tests/expected/annoGrator/pgSnpDbToTabOut.txt
  • lines changed 4, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToTabOutShort.txt
  • lines changed 4, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/hg/lib/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoColumn.h
  • lines changed 26, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoFilter.h
  • lines changed 65, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoFormatTab.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoFormatter.h
  • lines changed 60, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoGrator.h
  • lines changed 52, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoGratorQuery.h
  • lines changed 44, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoRow.h
  • lines changed 36, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/annoStreamer.h
  • lines changed 88, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/inc/options.h
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoColumn.c
  • lines changed 41, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoFilter.c
  • lines changed 184, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoFormatTab.c
  • lines changed 149, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoFormatter.c
  • lines changed 119, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoGrator.c
  • lines changed 194, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoGratorQuery.c
  • lines changed 161, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoRow.c
  • lines changed 57, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/annoStreamer.c
  • lines changed 96, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.
• src/lib/options.c
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output.