v311

Code changes:

• Fixed a bug in asParse just introduced, not in field. Brian
• Added ability to print out fieldCount from bigBedInfo utility. Brian
• Fixed bug in twoBitMask when bed file goes beyond end of chromosome (#14669). Brian
• Added check to hubCheck so that it complains if "type bigBed #" specifies more fields than are in the bigBed file. Brian
• Fixed the stacked bar chart display to stack in the order the wiggles appear in hgTrackUi. Brian
• Fixed disappearing bigBed items when zoomed way in (#14045). Brian
• Stopped putting conservation settings in cart in hgTracks when there is no reason to (#14622). Brian
• Added support for both '=' and 'X' in BAM cigars (#14593). Brian
• Created new UI framework based on ReactJS and ImmutableJS, with toy/demo app hgChooseDb and Annotation Integrator interface hgAi (#14579). Angie
• Added support for minimal biocuration tables (containing at least 'term', 'description' and optional 'url') that can be used to create track labels, mouseovers, and links on track configuration and detail pages (substituting for cv.ra + metaDb + hgEncodeVocab functionality). Tracks use these via new trackDb settings 'subGroupMetaTables' (for composites) and 'inputFieldMetaTables' (for 'combined' tracks that use 'inputTrackTable' setting). This will be used by the hg38 DNase tracks. Code for this feature is in hgTrackUi and hgc. Kate
• Fixed bug in hgTrackUi subtrack table sort. It will now correctly sort in columns besides the primary sort column (#14723). Kate
• Extended hgTrackUi sortable subtrack table to support a column showing subtrack color (sorted on hue). This allows the trackDb setting 'showSubtrackColorOnUi' to be used with the 'sortOrder' setting (#14723). Kate
• Made some minor hgTracks changes to label color selection, prompted by use of color spectrum with light colors in large multiwig and related tracks. These changes set black left labels on full visibility aggregate=none multiwigs, and black center label on dense visibility composite tracks (previously color of first displayed subtrack) (#14750). Kate
• Fixed menu link to hgTables so that it automatically selects the group track and table (now fixed for tracks in containers) (#14173). Galt
• Added a check for duplicate column names in .as autoSql table definition parser (#14727). Galt
• Added Robert Hubley's latest updates to the new Repeat Masker display. These changes provide all visibilities (dense/squish/pack/full) for the new track (#9741). Hiram
• Added support to gff3ToGenePred tool to allow creating a GenePred from a GFF3 file that includes a CDS child of a transcript or mRNA. Mark
• Throw an error when axtChain tool takes in PSL files with an explicit target. Mark
• Fixed bug where using setvbuf when mustOpen was called with magic file name 'stdout'. Previously this caused file corruption. Mark
• Added a "data last updated" value to the schema page in hgTables (#14647). Chris

Data changes:

• Updated uniProt and proteins databases for new UCSC genes release. Brian
• Added autoSql file so schema link on mafSnp160way describes fields. Brian
• Added microarray tracks for hg38: GNF and U95 and U133 (#14640). Brian
• Tweaked snp142 all.joiner (#14189). Angie
• Added new 'wgEncodeCell' table -- has cell types from ENCODE, with short descriptions and vendor URL, along with additional curation from ENCODE2 and ENCODE3. This will be released with the hg38 DNase tracks (#14731, #14732, #14733). Kate.
• Updated clinVar track for hg19 (#14045). Max
• Finalized the Retroposed Genes V6 (mm10), and V9 (hg38) tracks (#14719, #14720). Rachel
• Added a few new sequences to Ebola/eboVir3 assembly (#14278). Hiram
• Added GRCh38 Patch 2 (#14167). Hiram
• Completed new browser for Bonobo, panPan1 (#8231). Hiram
• Completed new browser for Tarsius syrichta, tarSyr2 (#14410). Hiram
• Moved the GWIPS-viz Ribo-seq track to the Expression track group and corrected description page (#14066). Steve