File Changes for angie

v268_preview2 to v268_base (2012-05-29 to 2012-06-05) v268

• src/hg/hgTables/vcf.c
  • lines changed 18, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    Bug #8048: Fix suggested by Tim: add a class to ldUi's inversion checkboxes,and detect that class when marking changes in subCfg.js. Also found an slSort
    that was missing & for its first arg, resulting in weird sorting of subtracks
    for inversion checkbox display.
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 1, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 45, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): UI seems to work on IEand Chrome now too, not just FireFox. Lessons learned: 1. event bubbling
    behavior is unique to each browser; 2. If there's a jquery way to do it,
    use jquery.
    
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/js/hgVarAnnogrator.js
  • lines changed 38, context: html, text, full: html, text
    Larry refactored hgCustom's loading image and message to ajax.js,so use that in hgVarAnnogrator.js instead of copied hgCustom code.
    
  • lines changed 53, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): UI seems to work on IEand Chrome now too, not just FireFox. Lessons learned: 1. event bubbling
    behavior is unique to each browser; 2. If there's a jquery way to do it,
    use jquery.
    
  • lines changed 1, context: html, text, full: html, text
    Typo fix.
• src/hg/js/subCfg.js
  • lines changed 5, context: html, text, full: html, text
    Bug #8048: Fix suggested by Tim: add a class to ldUi's inversion checkboxes,and detect that class when marking changes in subCfg.js. Also found an slSort
    that was missing & for its first arg, resulting in weird sorting of subtracks
    for inversion checkbox display.
    
• src/hg/lib/bbiChroms.as
  • lines changed 1, context: html, text, full: html, text
    Tweaking column name to be consistent with prior BAM usage & code.
• src/hg/lib/bbiChroms.sql
  • lines changed 2, context: html, text, full: html, text
    Tweaking column name to be consistent with prior BAM usage & code.
• src/hg/lib/hdb.c
  • lines changed 44, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/lib/tests/expected/annoGrator/vcfEx1.txt
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/hg/lib/tests/expected/annoGrator/vcfEx2.txt
  • lines changed 36, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/makeDb/doc/hg18.txt
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/inc/annoFormatter.h
  • lines changed 8, context: html, text, full: html, text
    Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
    and pass them to each formatter.
    
  • lines changed 15, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/inc/annoOption.h
  • lines changed 22, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/inc/annoStreamer.h
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/inc/options.h
  • lines changed 2, context: html, text, full: html, text
    options.h depends on common.h because it uses boolean.
• src/lib/annoFormatTab.c
  • lines changed 34, context: html, text, full: html, text
    Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
    and pass them to each formatter.
    
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/lib/annoFormatter.c
  • lines changed 99, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/lib/annoGratorQuery.c
  • lines changed 12, context: html, text, full: html, text
    Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
    and pass them to each formatter.
    
• src/lib/annoOption.c
  • lines changed 97, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/lib/annoStreamVcf.c
  • lines changed 8, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/lib/annoStreamer.c
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.