v297
- v297 Preview 1 - 3 March 2014
- v297 Preview 2 - 10 March 2014
- v297 Final - 17 March 2014
Code changes:
- Added 100X zoom out button to main tracks image (#7475). Bob
- Improved error messages for directly uploaded bigData Custom Tracks (#12747). Angie
- Fixed broken VCF intersection in the Table Browser (#12777). Angie
- Fixed coord-arithmetic in VAI that caused crash for user (#12778). Angie
- Fixed custom coloring of SNPs by exceptions in hgTracks (#12793). Angie
- Added support for (small) plain VCF custom tracks to the: Table Browser, Tracks page, details pages, VAI, and Custom Tracks (#12416). Angie
- Trim identical bases on right of indel alleles to prevent false overlap after observing this in multiple MLQ users' VCF files in: Tracks page, details pages, VAI. Angie
- Fixed renaming bug that applied only with USE_BAM=1, KNETFILE_HOOKS=0 (#12827). Angie
- Code review prompted cleanup of some unneeded #ifdefs (#6235, #12850). Angie
- Several fixes for minor bugs, hgSession/makefile, strict compiler warning. Angie
- Fixed display of names in GENCODE 2-way pseudogenes (#12824). Mark
- Fixed bug in GTF to genePred conversion where an assertion was triggered when the GTF had a spliced stop codon where the exon containing the first part of the stop codon only consisted of the stop codon bases. For example, a two-base exon where with two bases are the first two bases of the stop codon. Mark
- As per Ted Goldstein's code and request: altered the way ajax return from update of tracks in the hgTracks image is parsed. This should have no noticeable effect on standard browser function but will be more tolerant of differences during MedBook redirect to our browser (#12829). Tim
- Added hgsid back into the hgTracks URL (as shortened by history plug-in). This solves bug in one edge case where history plug-in uses URL directly (rather than handing it to our code). The added benefit is that copied URLs will be able to call up the same set of tracks/settings as (currently) associated with the hgsid (#12819). Tim
- Simple change to prevent top menu from wrapping, which broke the menu. This bug was reported by Bob and was seen when the browser window was small (as necessary for overhead projections) (#12122). Tim
- Added random session key for greater security of cart data (#9108). Galt
- Added bottleneck delay to cartDump (#9108). Galt
- Fixed GTF output from Table Browser with BAM Custom Tracks and hubs (#12737). Galt
- Fixed bug in bedDetail that prevented long HTML fields (#12875). Brian
- Fixed code in bigWigCat that broke BioPerl. Brian
- Ongoing work on Genome Browser in a Box (GBiB) (#11957). Max
Data changes:
- Released new human assembly: GRCh38/hg38 (#11681). Hiram
- Set up chain/net composites to use same definitions between hg19 and hg38 (#11681). Hiram
- Fixed bug in script then regenerated snp138CodingDbSnp for cow, chicken, pig, and dog (#12490). Angie
- Added catch-all LRG transcript search for LRG region terms (#12882). Angie
- Update canonical motif table for Factorbook in Transcription Factor ChIP Clusters track (#12551). Kate
- Ongoing work on farm animal QTL tracks (#10954). Pauline
- Update to v68 COSMIC track (#10158). Hiram
- Added Gene track to Lamprey, petMar2 (#9153). Hiram
- Cleaned all compile errors of source tree on Mac OSX (#12209). Hiram
- Alphabetized all tracks on hg18 browser except for tracks that are on by default which appear first within each track group (#7343). Hiram
- Ongoing work on UCSC Genes build for hg38 and mm10 (#12832, #12639). Brian
- Lifted GENCODE Genes from hg19 to hg38 (#12674). Brian