v333
- v333 Preview 1 - 9 May 2016
- v333 Preview 2 - 16 May 2016
- v333 Final - 23 May 2016
Code changes:
- Added 'RNA-Seq Expression' section to hgGene, that displays GTEx tissue-specific gene expression in a box-plot graph. Support default collapsed sections of hgGene. Set microarray section to default off (and change label to 'Microarray Expression' (#17244). Kate
- Add measureTiming support to hgGene. Kate
- Add settings to improve display of large composite tracks with metadata (hoverMetadata) and many or fixed track colors (darkerLabels), in support of GTEx Signal Hub (#17314). Kate
- Display metadata on details page directly (don't require click on metadata link) in support of GTEx Signal Hub (#17314). Kate
- Final polish for GBiC product (#14399). Max
- Fixed some minor sql injection in hgTracks and hgc. Galt
- Fixed signal handling in https made compatible with OSX (#17362). Galt
- Restored cytoBand fuzzy search (#17253). Angie
- Changes to new Gateway: Initialize oldVars so position is set correctly when db=... is a CGI param (#17267); Don't crash on missing hub description URL (#17315). Angie
- Fix hgCustom so that it does not crash on empty cart (#16174). Angie
- Fix hgTables crash when intersection settings were carried over from local db to hub. Angie
- Changes to hgSession / hgLogin / cart: if login is enabled, attempt to add a new column keyList to gbMembers and store random keys there, similar to userDb.sessionKey for hguid cookie. If able to add the column, use random keys to verify login (#17327). Angie
- Fix track search for the new mm10 UCSC Genes (#15315). Jonathan
- Started implementing Chromatin interaction display mode; Libified ave program (#15232). Brian
- Use autoscale and maximum mode as defaults for BAM density graphs (#952). Brian
- GenBank changes: default to looking for genbank metadata tables in hgFixed. Brian
- Fixed a bug with stacked wiggles where only one dataset is selected (#17281). Brian
- Support bigPsl, bigChain, and bigMaf as custom tracks. Brian
- Sped up the display of ORegAnno tracks in large regions, now that we load the color table once instead of once per track item (#17278). Jonathan
- Ongoing work on CIRM: cdwSubmit, cdwMakeEnrichments, cdwMakeValidFile, cdwLib, cdwValid: changes to cdwSubmit and adding in a new vocabulary term (#17334); renamed maniMani program (#16113). Chris
Data changes:
- Completed new assembly browser for chicken, galGal5 (#17168). Hiram
- Ongoing work on NCBI RefSeq Gene track for hg38 (#13673). Hiram
- Created GRCh38 patch 7 (#17134). Hiram
- Created GRCm38 patch 4 (#16414). Hiram
- Added 'chainCleaner' code from Michael Hiller to source tree (#17286). Hiram
- Added 145-way multiple alignment on hg38 from Michael Hiller (uses the new 'chainCleaner' procedure) (#17286). Hiram
- Created liftOvers from rn6 and danRer10 to galGal5 and galGal4 (#17015). Hiram
- Created liftOvers for ce8 to ce11. Hiram
- First draft of big* format docs. Brian
- Added some additional clustering for the PFAM track. Brian
- Created public track hub of GTEx Signal Data, hosted on hgdownload (#15647). Kate