File Changes for angie
switch to commits view, user indexv268_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.
- 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.
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