v276

Code changes:

• Fixed bug in hgHubConnect that was preventing errors from showing up (#9609). Brian
• Using UDR for genbank transfer to euronode. Brian
• Fixed genbank searching for assemblies without all_mrna table which used to silently fail. Brian
• Fixed Table Browser to display only the uniProt and proteome databases, not swissProt and proteins (#8133). Brian
• Pulled some logic out of hgc.c and put it in numtsClick.c (#8533). Chin
• Added hgWiggle utility to build (#9548). Chin
• Reduced privileges for the default MySQL user (hguser) to accommodate requirements for MySQL 5.1 and 5.5 (#9565). Galt
• Fixed a bug in autoXml so that it works now with XML name spaces. Jim
• Moved the full text index (trix) command line driver from one-shot to a real place in the source tree and gave it a better name and improved comments. Jim
• Added bedDetail track type to allow composite trackDb configuration options. Hiram
• Added code from Robert Hubley to src/hg/liftUp/liftUp.c to allow lifting of RepeatMasker .align file types. Hiram
• Added dropdown items to 'Mirror' menu to enable users to switch between geographic mirror sites (US and Europe). These will be visible only on the official sites, and will be enabled by hg.conf settings once the Euronode is fully deployed (#7477). Kate
• Fixed display problem for VCFs with mixed haploid status (e.g. chrX). Angie
• Fixed crash when per-chromosome BAM files are not available for all chroms. Angie
• Hosting samtabix git repository at UCSC (#6336). Angie
• Ongoing work on Variant Annotation Finder (added annoStreamBigBed) (#6152). Angie

Data changes:

• Created centromere browser. Max, Karen & Jim
• Nuclear mitochondrial sequences (Numts) tracks for cow (bosTau6) and pig (susScr2) (#8533). Chin
• Completed papAnu2 (olive baboon) assembly (#8166). Chin
• Completed petMar2 (lamprey) assembly (#9153). Hiram
• Converted ISCA composite to a multi-view track. Tim
• Updated CCDS database schema. Brian
• Updated mm10 UCSC Genes to use rn4 and ce6 (not rn5 and ce10) (#7045). Brian
• DGV data update, hg17 hg18 hg19 (#9401). Angie
• Reloaded snp137 with corrections from dbSnp, hg19 (#8360). Angie