·
272 commits
to master
since this release
This is the v482 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Change the hubConnect page so it no longer redirects.
- Improving mouseover of genePred tracks, adding hint to zoom in more to show cDNA positions, and a link to a new doc html page that explains what we mean by "phase 0/1/2".
- Added right-click Track Description feature in hgTracks.js.
- BAM tracks now go into coverage mode if maxItems is exceeded. Also added a cap to the number of items that will be loaded (BAMMaxItems).
- It is now assumed that the RGB value in the ninth field of a bed should be treated as a color.
- Allow .bigBed file extension to work with featureBits.
- Fixed hgBlat table of alignments not available once browsing. This fixes both native blat track and ct blat track.
- Changes to our bottleneck system to better recognize and penalize heavy bot activity on our servers.
- Anti-bot work: wait for 10 seconds on. Added hg.conf that triggers apache log entry when a user arrives without cookies, and added bytedance bot to robots.txt.
- New tool tabToBed: give it a .tsv file and it will guess what the fields with chrom, start, end, name, or give it the names of these fields and it will make an .as file and a .bed file to make a bigBed from the .tsv.
- GBIC changes: a few small changes for OSX, adding freetype for all linuxes, fix straw.cpp for new g++, allow builds on the beta tag when not on the beta branch for mirrors, always use mariadb and removing mysql_config dependency, removing udr, always install curl just in case, redoing the whole Dockerfile using newer commands, address the root user problem for mariadb, and other changes.
- Fixed buffer overflow in fixed-size mouseover buffer by making it a bigger fixed size.
- "hubtools up" no longer re-uploads a file into Hubspace if it's already there.
- hgVai: fixed corner cases surfaced by running vai.pl on EVA snps (40 assemblies, 909M variants).
- Improvements to wuhCor1 big tree build process.