v348

Code changes:

• New Variant Annotation Integrator script, vai.pl, added to userApps (#12216). Angie
• New zoom dialog enhancements allowing multi-highlights with custom colors options and modifier keys for quick addition and removal (#19118). Max
• Support for barChart/bigBarchart track type, to be finalized in next release (#18736). Kate
• Add GO button to Configuration subsection of GTEx Track Settings page (#18556). Kate
• Implementation of -long option to faToTwoBit to allow 64 bit indexes (#19110). Brian
• Addition of ability to add metadata to track hubs using a tab separated file (#18183). Brian
• hgTracks: mention HGVS in position/search watermark for human assemblies (#19215). Angie
• hgTracks: add highlighting of position for padded searches like HGVS and SNP (#19215). Angie
• DAS server can now contact a bottleneck server to moderate usage (#19193). Jonathan
• Ongoing work on custom blat tracks (#2811). Brian
• Updated auto scripts that generate text or HTML for hgdownload files and html description pages, to construct URLs to soe.ucsc.edu where they used to be cse.ucsc.edu (#19134). Hiram.
• Fix for how GBiB looks for track hub public.ix file (#19195). Brian
• Added expMatrixToBarchartBed to input coordinates, metadata, and matrix files and produce a bed6+4 barChart display (#19155). Christopher
• hgTables: fix: make sure position warning appears (#19190). Angie
• hgVai: fix: variant row limit was not applied to pgSnp file (#12216). Angie
• Fixed backwards compatibility for udcCache after SevenBridges changes. Restored HEAD as primary date/size check. (#19240). Galt.
• Added fast public-domain SHA1 hash routine. Galt
• Made tagStormCheck and tagStormToSql check for use of SQL reserved words. Made a library module, lib/sqlReserved.c, that assists with process. Jim
• CIRM: porting tagStorm library to python. Max
• CIRM: for data warehouse made utilities for renaming file names (submit file names, not license plates) and renaming datasets. Jim

Data changes:

• Rebuilt UCSC Gene Pfam track (#19207). Brian
• Building browsers for: xenTro9, xenLae2, criGriChoV1 (#19151 #17435 #19228). Hiram
• Not yet for release, built an assembly diagnostic track on all hgwdev genome browsers Gap overlaps summary at: http://genomewiki.ucsc.edu/index.php/GapOverlap Hiram.
• Not yet for release 4-way alignments on each of: tupChi1, galVar1, hg38, mm10. Hiram.
• TransMap and GENCODE track work. Mark