Commits for angie

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

• Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
  • src/hg/makeDb/doc/hg19.txt - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/pgSnp.html - lines changed 229, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/pgSnpHgwdev.html - lines changed 331, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra - lines changed 463, 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/makeDb/trackDb/tagTypes.tab - lines changed 3, context: html, text, full: html, text
• A couple more updates for hg19 Personal Genome Variant tables. refs #683
  • src/hg/makeDb/doc/hg19.txt - lines changed 7, 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/inc/trackDb.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 4, context: html, text, full: html, text
• A couple data updates for hg18 Genome Variants -- much less extensive than hg19.
  • src/hg/makeDb/doc/hg18.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/pgSnp.html - lines changed 15, context: html, text, full: html, text
• oops, forgot to clean up qLm -- added now. for #6152
  • src/inc/annoGrator.h - lines changed 1, context: html, text, full: html, text
  • src/lib/annoGrator.c - lines changed 13, context: html, text, full: html, text
• When running from command line, SCRIPT_NAME is undefined (unless one purposefully sets it). Avoid segv.
  • src/lib/cheapcgi.c - lines changed 4, context: html, text, full: html, text
• Adjustable font size for collapsible sections.
  • src/hg/inc/jsHelper.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 11, 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/annoStreamBigBed.h - lines changed 1, context: html, text, full: html, text
  • src/lib/annoStreamBigBed.c - lines changed 97, 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/snp132Ext.as - 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/hgVai/hgVai.c - lines changed 1105, context: html, text, full: html, text
  • src/hg/hgVai/libifyMe.c - lines changed 441, context: html, text, full: html, text
  • src/hg/hgVai/libifyMe.h - lines changed 40, context: html, text, full: html, text
  • src/hg/hgVai/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgVaiHelpText.html - lines changed 7, context: html, text, full: html, text
  • src/hg/inc/annoFormatVep.h - lines changed 38, context: html, text, full: html, text
  • src/hg/inc/annoGratorGpVar.h - lines changed 23, context: html, text, full: html, text
  • src/hg/inc/annoStreamDb.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 568, context: html, text, full: html, text
  • src/hg/lib/annoGratorGpVar.c - lines changed 131, context: html, text, full: html, text
  • src/hg/lib/annoStreamDb.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/annoStreamWig.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/gpFx.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 77, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTests.mk - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 26, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/tests/input/annoGrator/moreVariants.pgSnp.tab - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/tests/input/annoGrator/pgForTestingGpFx.pgSnp.tab - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 5, context: html, text, full: html, text
  • src/lib/annoStreamVcf.c - lines changed 44, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 38, context: html, text, full: html, text
• Added a couple of Galt's new sqlSafef's.
  • src/hg/hgVai/hgVai.c - lines changed 2, context: html, text, full: html, text