v275
- v275 Preview 1 - 15 Oct 2012
- v275 Preview 2 - 22 Oct 2012
- v275 Final - 29 Oct 2012
Code changes:
- Made errors in hub.txt and genome.txt show up as warnings in hgTracks (#8848). Brian
- Changed pslToBed to set thickStart and thickEnd to chromStart for non-coding beds (#7045). Brian
- Mapped all characters other than alnum, dash, and underbars to underbars in track names in track hubs (#9254). Brian
- Changed bedExact library method to look at thickStart and thickEnd (#7045). Brian
- New compilation option, now default at UCSC: instead of separately downloading, patching and building samtools and tabix, we can use the new samtabix package (https://github.com/AngieHinrichs/samtabix) which contains combined, pre-patched samtools and tabix. See kent/src/product/README.building.source (#6336). Angie
- On details page for VCF data, if name looks like dbSNP or dbVar ID, make an external link. Angie
- Fixed recently introduced liftOver bug for bedPlus data. Angie
- Fixed HTML double-encoding problem in VCF details. Angie
- Added three missing NULL checks, fixed two stricter-gcc warnings. Angie
- Removed support for 32-bit CGI build (#9403). Chin
- Made items in Ensembl Assembly track searchable (#9297). Chin
- Released Track Database Definition Documentation (for generic trackDb settings and for Track Hubs) (#5088, #5590). Tim
- Fixed support for "parent" setting in superTrack child (#9150). Tim
- Made a command line interface to the "trix" free text search library. Jim
- Labeled BLAT for a new public release, which includes about 10 small bug fixes from the last year or two. Jim
Data changes:
- Used CCDS 103.0 for hg19. Brian
- Changed default genbank parameters to *not* build "Other mRNA" (xenoMrna table). Brian
- Automated ISCA load (#5172). Brian
- Corrected frames reloaded for the mm10 60-way conservation track (#8876). Hiram
- Fixed quality track overrides to correctly indicate maximum value in the data (#7681, #8887). Hiram
- Added utilities to utils build for users: faRandomize, paraSync, bedExtendRanges, makeTableList, hgGcPercent. Hiram
- 1000 Genomes Variant Calls: reloaded data, added brief methods summary with links to additional reading (#7964). Angie
- Started browser for lanclet braFlo2 (#9402). Hiram
- Finished browser for lamprey petMar2 (#9153). Hiram
- Finished browser for white rhino cerSim1 (#8752). Hiram
- Finished browser for rhesus macaque (Macaca mulatta) rheMac3 (#6144). Chin
- Finished browser for olive baboon papAnu2 (#8166). Chin