v340
- v340 Preview 1 - 3 Oct 2016
- v340 Preview 2 - 9 Oct 2016
- v340 Final - 19 Oct 2016
Code changes:
- New disconnect button for track hubs from the main browser (#15973). Brian
- Improved HGVS position search (#15071). Angie
-coding intron/UTR coords -ins/del/dup etc (change is no longer fully parsed) -fuzzy HGVS match (missing ., NM_ accession with p. description) -support gene symbol and codon number or gene symbol c. -use NCBI's RefSeq alignments when available -use new table chromAlias when available for NC_*g.* terms.
- VCF parser support for VCFv4.2 additions (#15625). Angie
- VCF genotype parsing fix (#18219). Angie
- Accommodate dbNSFP slight format change (#18199). Angie.
- Optimize display of MAFs to use much smaller MAF in hg38 if only default species are on in 100way (#18073). Brian
- Fix for urls using hideTracks=1 to recognize and adjust super track visibilities (#18146). Brian
- Fix for a problem in mafGene (CDS FASTA output) when translating 1bp exons. Brian
- Begin implementation of tagStorm support in track hubs, added a utility to convert metadata lines in a track hub to a RA file (#18183). Brian
- htmlPage now decodes attributes which we are now encoding against XSS and fix for encoding of pipe character in static page URLs (#18077). Galt
- Fixes for very early warning html handler to encode printf parameters, and missing content-type problem caused by errAbort with the wrong handler (#18162, #18163). Galt.
- CIRM:cdwSubmit - Put in a check for a necessary library environment variable (#17334). Chris
- CIRM:cdw*- Changed the autosql code to add in the cdwJointDataset c code. (#17870) Chris
- CIRM:cdwWebBrowse - Put in the changes for joint data sets, updating file permissions, flow charts and the overall page layout update. (#17334). Chris
Data changes:
- Repaired pfam tracks to solve off-by-one error (#18094). Brian
- Regenerated hg19 CDS FASTA downloads (#18180). Brian
- Added bigBed files gbdb/hg{19,38}/vai/snp147.bed4.bb to speed up hgVai's rs# ID matching (#18222). Angie
- Work on CRISPR tracks (#17235). Max
- Assembly work for chlSab2/Green Monkey/Chlorocebus, panTro5/Chimp/Pan troglodytes, and gorGor5/Gorilla/Gorilla (#11172,#17817,#17580). Hiram