Commits for angie
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v302_preview2 to v302_base (2014-06-23 to 2014-06-30) v302
- Added sqlQuickPairList for quick two-column queries.
- Adding sequence cache to annoAssembly (moving up from annoGratorGpVar).
- src/lib/annoAssembly.c - lines changed 18, context: html, text, full: html, text
- Added factorSourceAsObj for anno*.
- src/hg/inc/factorSource.h - lines changed 3, context: html, text, full: html, text
- src/hg/lib/factorSource.c - lines changed 23, 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/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 7, context: html, text, full: html, text
- src/inc/annoStreamer.h - lines changed 12, context: html, text, full: html, text
- src/lib/annoStreamer.c - lines changed 13, 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).
- 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/hgVai/libifyMe.c - lines changed 8, context: html, text, full: html, text
- src/hg/inc/annoFormatVep.h - lines changed 8, context: html, text, full: html, text
- src/hg/inc/annoStreamDbFactorSource.h - lines changed 17, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 135, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 44, context: html, text, full: html, text
- src/hg/lib/annoStreamDb.c - lines changed 28, context: html, text, full: html, text
- src/hg/lib/annoStreamDbFactorSource.c - lines changed 221, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 3, 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/hg17/trackDb.ra - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/trackDb/opossum/trackDb.ra - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra - lines changed 4, 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
- Hooking up recent dbSNP builds to snp125Methods... really should make a snp125 track type for these.
- src/hg/hgTracks/simpleTracks.c - lines changed 8, 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
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