v341
- v341 Preview 1 - 24 Oct 2016
- v341 Preview 2 - 31 Oct 2016
- v341 Final - 7 Nov 2016
Code changes:
- New trackDb setting darkerLabels allows left labels on the track display to have a somewhat darker color than the track display itself, useful where the track color might be too light for readable lablels (#18186). Kate
- New hgc special link out to ExAC site like ExAC: 21:24451624 A/T And code to not display empty placeholder names when no rsID (#18284). Angie
- Enhancements to hgTracks/hgc VCF: adapted code from Belinda Giardine (#18275). Angie
For TUMOR/NORMAL VCF, show tumor allele counts in mouseover.
Infer genotypes from SGT tag for VCF from Strelka.
- hgTables bugfix: intersection wasn't supported for bigDataUrl tracks (#18289). Angie
- Enhance hub checking to see if hubs have identical track names (#18317). Brian
- Fixed a problem in selecting genePreds in maf detail page (#18283). Brian
- Added bigChain.as and bigLink.as to source (#17325). Brian
- Work on developing hubToMetaRa (#18183). Brian
- Option added to genePredCheck to get chromsome sizes from file. Mark
- Option added to pslCheck to strip qName uniqueness modifiers. Mark
- Changed hdb.h to remove prototypes for unimplemented functions (#14715). Jonathan
- Finalized bamToPsl command started by Jim (#13673). Hiram
- Position/search bugfix (patch) around mysql & refGene, assembly hubs and dbs that don't have refGene (#18240). Angie
- Update to htmlCheck and the lib/htmlPage.c to make the validation more compatible with modern web pages. Specifically it now checks DIV, SCRIPT, and SVG tags for nesting. It no longer checks that INPUT and BUTTON and related tags are inside of FORMS. It is more relaxed about the HEAD and BODY tag placement. Jim
- CIRM: minor work mostly to do with changing metadata vocabularies to MISCE standards. Jim
- CIRM: cdwManiFastqToKallisto -updating the transcriptome pointed to by the script (#17630). Chris
- CIRM: cdwValid -changing the list of valid tags from UCSC tags to MISCE tags (#17334). Chris
- CIRM: cdwWebBrowse, cdwGetMetadataAsFile, cdwLib -code to support view and download of ra and tsv formats of users metadata (#17870). Chris
Data changes:
- Final small changes for CRISPR tracks on hg19, hg38, dm6, danRer7, mm10, sacCer3, rn6 (#17235). Max
- Ensembl genes v86 add to the pushQ (#18240). Hiram
- Mouse strain assembly hub added for QA from hgdownload (#13553). Hiram
- dm3 to droSim2 liftOver per user request (#18269). Hiram
- galGal3 to galGal5 liftOver per user request (#18256). Hiram