File Changes for angie

v284_base to v285_preview (2013-05-27 to 2013-06-04) v285

• src/hg/hgVai/hgVai.c
  • lines changed 1105, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    Added a couple of Galt's new sqlSafef's.
• src/hg/hgVai/libifyMe.c
  • lines changed 441, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/hgVai/libifyMe.h
  • lines changed 40, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/hgVai/makefile
  • lines changed 15, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 7, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/inc/annoFormatVep.h
  • lines changed 38, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 23, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/inc/annoStreamDb.h
  • lines changed 1, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/inc/jsHelper.h
  • lines changed 5, context: html, text, full: html, text
    Adjustable font size for collapsible sections.
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683
• src/hg/lib/annoFormatVep.c
  • lines changed 568, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 131, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/annoStreamDb.c
  • lines changed 5, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/annoStreamWig.c
  • lines changed 1, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/gpFx.c
  • lines changed 12, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683
• src/hg/lib/jsHelper.c
  • lines changed 11, context: html, text, full: html, text
    Adjustable font size for collapsible sections.
• src/hg/lib/snp132Ext.as
  • lines changed 1, context: html, text, full: html, text
    Changing the type of strand to match fullBed.as so bedToBigBed willaccept this as 'bed 6 + ' autoSql.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 77, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 5, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 26, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 12, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 14, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/tests/input/annoGrator/moreVariants.pgSnp.tab
  • lines changed 5, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/tests/input/annoGrator/pgForTestingGpFx.pgSnp.tab
  • lines changed 13, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/lib/trackDbCustom.c
  • lines changed 4, context: html, text, full: html, text
    Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683
• src/hg/makeDb/doc/hg18.txt
  • lines changed 16, context: html, text, full: html, text
    A couple data updates for hg18 Genome Variants -- much less extensive than hg19.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 80, context: html, text, full: html, text
    Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
  • lines changed 7, context: html, text, full: html, text
    A couple more updates for hg19 Personal Genome Variant tables. refs #683
  • lines changed 7, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • lines changed 15, context: html, text, full: html, text
    A couple data updates for hg18 Genome Variants -- much less extensive than hg19.
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • lines changed 229, context: html, text, full: html, text
    Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
• src/hg/makeDb/trackDb/human/hg19/pgSnpHgwdev.html
  • lines changed 331, context: html, text, full: html, text
    Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
• src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
  • lines changed 463, context: html, text, full: html, text
    Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, context: html, text, full: html, text
    pgSnp tracks are now declared as 'type pgSnp', so add pgSnp to theacceptable types for pgSnp-related tags.
    
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/inc/annoGrator.h
  • lines changed 1, context: html, text, full: html, text
    oops, forgot to clean up qLm -- added now. for #6152
• src/inc/annoStreamBigBed.h
  • lines changed 1, context: html, text, full: html, text
    Fixed implementation of maxItems. To reduce the delay before getting thefirst item in range, now bbi queries are limited to 100,000 items at a time,
    so now there is a series of "chunk" queries instead of one query per region
    or chromosome. for #6152
    
• src/inc/vcf.h
  • lines changed 5, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/lib/annoGrator.c
  • lines changed 13, context: html, text, full: html, text
    oops, forgot to clean up qLm -- added now. for #6152
• src/lib/annoStreamBigBed.c
  • lines changed 97, context: html, text, full: html, text
    Fixed implementation of maxItems. To reduce the delay before getting thefirst item in range, now bbi queries are limited to 100,000 items at a time,
    so now there is a series of "chunk" queries instead of one query per region
    or chromosome. for #6152
    
• src/lib/annoStreamVcf.c
  • lines changed 44, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152
    
• src/lib/cheapcgi.c
  • lines changed 4, context: html, text, full: html, text
    When running from command line, SCRIPT_NAME is undefined (unless one purposefully sets it). Avoid segv.
• src/lib/vcf.c
  • lines changed 38, context: html, text, full: html, text
    New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
    predictions to identify which part of a gene, if any, is hit by each
    variant; several additional sources of annotations/predictions e.g.
    dbNSFP scores and conserved elements/scores; and several filters to
    constrain output to the variants most likely to have a functional effect.
    Along with the new CGI, there are various lib bugfixes and improvements,
    a new hg/lib/tests/ testcase, and some test file changes to accomodate
    data updates to both knownGene and the pg* tables in knownGene.
    refs #6152