v324

Code changes:

• Initial work on supporting bigMaf (remotely-hosted multiple alignment file) data type in the browser (#15935). Brian
• Initial support for GTEx gene expression and related tracks (#15645). Kate
• Fixed a bug in bedToBigBed when -tabs was specified which was ignored in index build. Brian
• Ongoing work on fixing source tree to eliminate warnings for -Wunused-but-set-variable (#16121). Hiram
• Added some new scripts used in the assembly hub pipeline. Hiram
• Fixed loading bigWig files from local dir via hg.conf option. Max
• Added drop-down menus to the Genomes and Genome Browser menus (#16022). Max
• Fixed a non-root apache installation issue (#16099). Max
• Fixed a GBiB error on VMWare and an old GBiB bug in the table browser (#16187, #16158). Max
• When returning to a previously-visited assembly, take the user back to their old position when position="lastDbRef" (#16185). Max
• Provide a link back to the genome browser from BLAT results and link to the FAQ (#16173). Max
• Changed some absolute links into relative links for the benefit of mirror sites (#16099). Jonathan
• Ongoing work to support new ORegAnno tracks (#15957, #16257). Jonathan
• Fixed code so that relative links in CGIs are no longer confused by HTML base tags in included files (#16124). Jonathan
• Fixed bug in Data Integrator that broke output field selection for subtracks. Angie
• Improved test harness for anno* libs. Angie
• Ongoing work on CIRM scripts and programs. newPythonProg (#16156); rainbow.c and rainbow.h (#16216); makeExpMatrix (#16182) ; addMetaDataToJson (#16182); condenseMatrix (#16182); hgLoadSeq (#16034); rnaSeqToClustersPipeline (#16244); kallistoOnFastqMani (#16244). Chris

Data changes:

• Started work on genome browser for gorilla assembly, gorGor4 (#16220). Jonathan
• Fixed problem with snp142 (hg19, hg38). Erased incorrect allele frequencies for variants on the '-' strand with 1000GENOMES as a submitter. Angie
• Reloaded variants for 1000 Genomes phase 3. Angie