v293
- v293 Preview 1 - 18 Nov 2013
- v293 Preview 2 - 2 Dec 2013
- v293 Final - 9 Dec 2013
Code changes:
- Added support for back-button in hgTracks; it now supports history of "positions". Track configuration settings will only reflect current settings (#7473). Tim
- Enabled concurrent running of genbank initial loads and the automatic updater (#10357). Brian
- Added tests for repsAsMatch pslCDnaFilter flag. Brian
- Allowed track hubs to be more forgiving of poorly-formatted lines in txt file (#12267). Brian
- Fixed a bug in maf frames builder where blocks of one base were being ignored (#12173). Brian
- Updated login procedures to Decipher web site. Brian
- Fixed net.c for FTP subtleties regarding url-encoding and the leading slash in the path requested (#12315). Galt
- Fixed a new problem in hgTables caused by a recent bugfix to gffOut. This ensures that the exonCount, exonStarts, and exonEnds match (#12274). Galt
- Fixed bug seen only in IE10: white-on-white text in site menus and black-on-blue group headers (#11745). Tim
- Minor change to support non-standard UWash Exome Variants VCF data in hgTracks display tool tip (#9329). Tim
- Fixed https access problem with ENCODE Experiment matrix (#12169). Kate
- Fixed source tree build bugs, old existing code problems identified by new gcc compiler on Mac OSX (#9149). Hiram
- Added build scripts to the source tree that were local files in the build account. Hiram
- Added generic scripts for all the steps of trash cleaning for mirror site users. Hiram
- hgVai / anno* libs: Fixed incorrect use of NMD_transcript_variant: it means 'variant in a transcript that is *already* subject to NMD, not that the variant causes NMD. (#12205); Added ability to paste in rs# IDs as variants to annotate (#11460); Cleaned up logic for detecting/adding extra left base for indel in VCF; Added hgTrackUi links for tracks offered by hgVai (#11461); User request: don't truncate alt allele column so short; Made per-gene-track Artificial Example Variants (not only per-region); Added comment method to annoFormatters; Added comment about no items in region (#12278). Angie
- Enabled hyperlinks output for bedGraph and microarray tracks from Table Browser. (#12198). Angie
- Extended base/difference-coloring code to support LRG Regions, LRG transcripts (#11863). Angie
- Refactored hg/lib/jsHelper and moved json parser and object tree bits of it to lib/jsonParse. Jim
- Removed jsonGlobalsHash from library routines. Now it is restricted to hgTrackUi as part of above refactoring. Jim
- Ongoing work on Genome Browser in a Box (GBiB) (#11957). Max
Data changes:
- Created Microsoft Research Bing web search track (#12212). Max
- Updated GO database (#10492). Brian
- Lifted MGI QTL track from mm9 to m10 (#7040). Pauline
- Rebuilt UCSF Brain Methyl track on hg19 (with remapped vs. lifted
data from Ting Wang) (#2540). Pauline
- Loaded public hub for McGill Epigenomics Mapping Centre (#12132). Pauline
- Loaded public hub for Broad canFam3 (#12204). Pauline
- Display of motifs in Transcription Factor cluster and other type factorSource tracks (#9092). Kate
- Added mapping table to factorSource track (and peakCluster track details) that links factor (HGNC gene ID) to canonical motif in motif table and PWM. This was needed as some motifs are primary for multiple genes). The table is configured via new trackDb setting: motifMapTable. Kate
- Created 57 genome assembly hubs (#10272). Hiram
- Started work on Ensembl Genes v74 (#12288). Hiram
- Compelted LRG Regions and LRG Transcripts tracks for hg19 (#11863). Angie