v302
- v302 Preview 1 - 16 June 2014
- v302 Preview 2 - 23 June 2014
- v302 Final - 30 June 2014
Code changes:
- Added regulatory consequence-calling to VAI using ENCODE Clustered TFBS and DNase (#11461). Angie
- Fixed a few VAI bugs. Angie
- Fixed a bug in searching where supertracks were not displaying when a search term matched an item in the track (#13477m #13304). Angie, Tim
- Cleaned up details pages for Segmental Dups tracks (#13171). Matt
- Disallowed the setting 'idInUrlSql' in track hubs (#11296). Galt
- Cleaned up JavaScript code based on run through jshint (#13255). Tim, Angie, Kate
- Fixed hgTrackUi to better support ranges in *Filter settings. Kate
- Ongoing improvements with the build: finding static libraries on OSX Mavericks with homebrew installed components, eliminates the need to bother the user about MACHTYPE settings (#12209). Hiram
- Added Google Analytics code ('Universal' functionality) (#13120). Hiram
- New utility: bamSplitByChrom. It takes in a BAM file and splits it apart into multiple BAM files, one for each chromosome. Chris
- New utility: bamMerge. It takes in multiple BAM files and merges them into a single BAM file. Chris
- Added a new option to bamToFastq: -unmapped. It prints unmapped reads. Chris
- Fixed off-by-one pixel height problem with BED files generated by hgGenome (#13440). Galt
- Fixed a bug where hiding a track in certain conditions resulted in an error (#13165). Tim
- Updated trackDbDoc to make it clear that '-' are not allowed in track names. Tim
- Added 2 new tokens for trackDb URL setting which are for clicked item start and end (#13218). Tim
- Sped up image-only reload as seen on FireFox when there are many (50) tracks displayed (#13347). Tim
- Added functionality to the chains display to make directional arrows visible more often. Jim
- Removed an optimization for short seeks in lineFileSeek that was breaking in most cases. This bug only seemed to manifest in the ENCODE data warehouse. Jim
- Fixed pslPairs bug that was trashing memory. Brian
- Added descriptionUrl to hubPublicCheck -addHub command. Brian
- Edited Hub portal page to make it more understandable.
- Fixed some hub connection that was making the browser crash (#11633). Brian
- Fixed a bug in bigBed track item search. Brian
- Enabled bigBed item search on native bigBed tracks. Brian
- Fixed bug in Watson/Crick wiggle mode (#13474). Brian
- Ongoing work on GBiB (#11957). Max
Data changes:
- Added search on lincRNAsTranscripts for user (#13475). Angie
- Fixed overzealous STS Map search. Angie
- Cleaned up some search spec keywords that were erroneously included in some trackDb entries and tagTypes.tab. Angie
- Started work on 26-species Conservation Track for dm6 (#13461). Chin
- Completed data loading/transform, docs and track config for new ENCODE DNase Master Sites track from UW/AWG (#13230). Kate
- Rebuilt ENCODE Regulation DNase Clusters to address incomplete data problem, 'clusters' from a single cell type are now included (#13490). Kate
- Fixed misleading filenames in ENCODE downloads (SYDH mouse histone) (#13404). Kate
- Fixed metadata (control ID) of ENCODE datasets (HAIB TFBS) (#13476). Kate
- Created GRC Incident track for hg38 and fixed it on hg19, mm10, mm9, danRer7 (#12407). Hiram
- Corrected cytoBand track updated on hg38 (#13379). Hiram
- Updated master phylo tree: now at 174 species (#10272). Hiram
- Created Lamprey gene track (#13358). Hiram
- Finalization of Animal QTL tracks (#10954). Pauline
- Finalization of FaceBase track (#12606). Pauline
- Finalization of rat, rn5, conservation track (#8212). Pauline