v319
- v319 Preview 1 - 29 June 2015
- v319 Preview 2 - 6 July 2015
- v319 Final - 13 July 2015
Code changes:
- Added an hg.conf option for the galaxy URL (#12642). Max
- Fixed species order in hgMirror (#15473). Max
- Fixed search problem in VisiGene (#12038). Galt
- Added new menus to static pages (#15389). Jonathan
- Ongoing work on VAI: Don't rely on Facebook's CDN (for https) (#15557); Fixed file up load for IE 10 and 11 (#15609); Don't let NANs creep into wiggle averages (#15675); Fixed race condition that led to wrong db (#15681); Don't pop up an error when user navigates away from a page while ajax requests have not yet completed (#15533). Angie
- Fixed table name in schema link in Data Integrator when non-composite track does not equal table (#15676). Angie
- Added geneId to TransMap genes, with backwards compatibility for current TransMap tracks (#14574). Mark
- Added option to gtfToGenePred to include gene and transcript version number that now part of Ensembl GTF files in the gene/transcripts ids. Mark
- Fixed click-through on snake tracks to other genomes in MySQL-backed HAL browsers. Mark
- Fixed calculation of PSL match statistic in chainToPsl. Mark
- Fixed pslStats computation of query coverage. It was not counting based aligned to Ns. Mark
- Removed the printing of chrom names to stdout in netStats; it seemed like a spurious debug message. Mark
- Fixed bug in limit view DNA from peak clusters details page to named item (#15495). Kate
- Updated hubCheck and trackDbDoc code support for release of hub versioning (#10015). Kate
- Extended tool for nightly URL check of links in tables, checkUrlsInTable (#10318). Kate
- Added database name to trackLog statements (#15577). Brian
- Added a few refinements to the utility that builds the core knownGene tables (#14639). Brian
- Fixed a bug in the mafGene library that would fail on sparse maf blocks (#14639). Brian
Data changes:
- Automated the update of the clinvar track for hg19 and hg38 (#14045). Max
- Ongoing work on CNV Developmental Delay track for hg19, hg38 (#9391). Steve
- Cleaned up trackDb type of several tracks that had type 'bed N .' but are 'bed N +' (#15610). Angie
- Created V1 trackDbHub file and help docs, for first release of hub versioning (#10015). Kate
- Created CDS fasta alignments for hg38 GENCODE (#14639). Brian
- Made description of gene set in knownGene.as more generic (#14639). Brian
- Started work on 16 nematode browsers including a Conservation track for Caenorhabditis elegans (WBcel245,ce11). Hiram