File Changes for angie

v302_preview2 to v302_base (2014-06-23 to 2014-06-30) v302

• src/hg/hgTracks/simpleTracks.c
  • lines changed 8, context: html, text, full: html, text
    Hooking up recent dbSNP builds to snp125Methods... really should make a snp125 track type for these.
• src/hg/hgVai/hgVai.c
  • lines changed 313, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
  • lines changed 1, context: html, text, full: html, text
    Fixing bug found by Jonathan: with clean cart, when showing contents offilter section for Regulatory Elements, the multiselects didn't appear.
    Turns out that the 'force' argument of ddcl.reinit actually makes it do
    nothing! To avoid disrupting anything else, for now I'll just forgo force.
    refs #11461
    
  • lines changed 26, context: html, text, full: html, text
    Adding regulatory region to the functional role filter options.Thanks Jonathan for noticing that I forgot to do that!
    refs #11461
    
• src/hg/hgVai/libifyMe.c
  • lines changed 8, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 7, context: html, text, full: html, text
    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/hg/inc/annoFormatVep.h
  • lines changed 8, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/inc/annoStreamDbFactorSource.h
  • lines changed 17, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/inc/factorSource.h
  • lines changed 3, context: html, text, full: html, text
    Added factorSourceAsObj for anno*.
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    Added sqlQuickPairList for quick two-column queries.
• src/hg/inc/variant.h
  • lines changed 8, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/js/ddcl.js
  • lines changed 1, context: html, text, full: html, text
    Fixing bug found by Jonathan: with clean cart, when showing contents offilter section for Regulatory Elements, the multiselects didn't appear.
    Turns out that the 'force' argument of ddcl.reinit actually makes it do
    nothing! To avoid disrupting anything else, for now I'll just forgo force.
    refs #11461
    
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    In setTableRowVisibility, when changing a row from hide to show,trigger a 'show' event so other JS code can listen and make updates
    if needed (e.g. hgVai.c).
    
• src/hg/lib/annoFormatVep.c
  • lines changed 135, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 44, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/annoStreamDb.c
  • lines changed 28, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/annoStreamDbFactorSource.c
  • lines changed 221, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/factorSource.c
  • lines changed 23, context: html, text, full: html, text
    Added factorSourceAsObj for anno*.
• src/hg/lib/jksql.c
  • lines changed 14, context: html, text, full: html, text
    Added sqlQuickPairList for quick two-column queries.
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 3, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/variant.c
  • lines changed 28, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/inc/annoAssembly.h
  • lines changed 5, context: html, text, full: html, text
    Adding sequence cache to annoAssembly (moving up from annoGratorGpVar).
• src/inc/annoFilter.h
  • lines changed 22, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/inc/annoStreamer.h
  • lines changed 12, context: html, text, full: html, text
    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/lib/annoAssembly.c
  • lines changed 18, context: html, text, full: html, text
    Adding sequence cache to annoAssembly (moving up from annoGratorGpVar).
• src/lib/annoFilter.c
  • lines changed 122, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/lib/annoGrator.c
  • lines changed 14, context: html, text, full: html, text
    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/lib/annoStreamer.c
  • lines changed 13, context: html, text, full: html, text
    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.