v294

Code changes:

• Allow colons in both HTTP and FTP URLs (#12337). Galt
• In support of the back button, added the assembly, organism and position to the URL (#7473). Tim
• Fixed a bug where sort was alphabetical on numeric values. This caused tracks to jump to unexpected places in the display image (#12465). Tim
• Reversed table name check strategy: check normal name first, split tables last (#11957). Max
• Fixed BAM display where color-by-tag was turning blue in large regions (#12345). Angie
• Fixed VCF reader to not require '=' in metadata lines in versions before 4.1 (#12417). Angie
• Added bamFileAndIndexMustExist for better catching and reporting of BAM file errors (#12401). Angie
• Added paste/upload options to VAI: accepts rs# IDs (#11460). Angie
• Created New tool for bigWig manipulation: bigWigCat (#12372). DanielZ, Brian, Galt
• Changed code to use new Q matrix files from lastz_D tuning runs, axtChain lavToAxt lavToPsl updated and tests added (#12254). Hiram
• Fixed blastz-run-ucsc and doBlastzChainNet.pl to use packages of contigs in .2bit files to lastz operations improving efficiency of lastz/chain/net operations (#11681). Hiram
• Turned on default no-split behavior for hgLoadOut for rmsk tables (#11681). Hiram
• Fixed defaults for doRepeatMasker.pl HMMER engine to use 4 CPUs and 32 Gb memory during cluster run (#11681). Hiram
• Edited makeGenomeDb.pl script to place bbi files into the new default location (#11681). Hiram
• Sped up the Table Browser by fetching only the list of chromosomes used by the table instead of all chromosomes (#12318). Galt
• Moved Publications track into new "Phenotype and Literature" track group on hg19, rearranged priorities to display pubs at top, and rest (hide by default) in alphabetical order (#12362). Pauline
• Removed word "Tracks" from all track groups in hg19 (#12284). Pauline
• Split "Variation and Repeats" track group; created new "Repeats" group and moved several tracks into new group (#12284). Pauline
• Changed Genbank's alignment strategy to remove recognition of repeat-masked sequence. Brian
• Ongoing work on Genome Browser in a Box (GBiB) including a new CGI: hgMirror (#11957). Max
• Ongoing work to clean up build and compiles (#12254 and others). Hiram, Angie
• Ongoing work on Parasol. Jim, Galt
• Ongoing work on install scripts for mirrors (#9104). Hiram

Data changes:

• Completed liftUnder felCat5 to felCat4 (#12163). Pauline
• Completed work on GENCODE v19 for hg19 (#12452). Mark
• Completed Quantitative Trait Loci track for bosTau7, susScr3, and galGal4 (#10954). Pauline
• Updated Ensembl Genes to v74 for many assemblies (#12288). Hiram
• Updated master phylo tree for a total of 120 species (#10272). Hiram
• Updated CCDS database with new schema. Brian
• Started work on Cooper Developmental Delay track for hg19 (#9391). Pauline
• Started work on GRCh38/hg38 (#11681). Hiram
• Started work to lift cytoband track from hg19 to hg38. Pauline
• Ongoing work on Microsoft Research Bing web search track (#12212). Max