v303

Code changes:

• Changed all links in navigation bar and on static doc pages to relative links. This makes it so that it is no longer required to install the browser at the top level (#13555). Galt
• Removed udcTimeout from the cart at end of hgTracks. This prevents this debugging tag, which Stanford set for everyone for a while in early versions of their track-hubs-on-the-fly, from persisting and slowing down tracks involving bigDataUrls, and track hubs indefinitely. Jim
• Created new program, expData, which takes in expression data and creates a binary tree using a hierarchical agglomerative clustering library. The output is a .json file type intended for d3 visualizations. Chris
• Started work adding new Repeat Masker nesting visualization display code from Robert Hubley (#9741). Hiram
• Fixed hgLoadChain to use a correctly sized INDEX on tName (#13548). Hiram
• Changed the sort order for assembly hubs. Sort according to the orderKey value on the order of databases in assembly hubs. The default is to list in the order in genomes.txt (#13659). Brian
• Fixed a bug that listed unconnected unlisted hubs when a hub was broken. Brian
• Refactored hubCheck to support HAL library. Brian
• Fixed a bug when an assembly hub did not have a freezename (#13660). Brian
• Fixed a problem where sessions on assembly hubs would not hold onto custom tracks (#13078). Brian
• Added "retry hub" error message to hgHubConnect so broken hubs can be disconnected (#13523). Brian
• Added trackDb settings for initializing VCF track configuration. Angie
• Fixed bug in hgTracks so that it now checks for missing null in factorSourceLoad. Angie
• Added missing call to setUdcCacheDir at startup to hgGene, hgConvert, hubCheck. Angie
• Fixed bug where in some circumstances, users get a blank cookie value (#13530). Galt
• Fixed bug in TF ChIP-seq track: suppress display of a motif for a TF peak whose highest-scoring motif lies outside the viewing window (#13318). Kate
• Bug fixes for VAI tool: first character of symbolic alt alleles were sometimes skipped; trailing quote was not stripped from FILTER header lines' descriptions (#13614); incorrect calls for large deletion; was calling frameshift instead of stop_gained when insertion makes a stop codon. Angie
• Ongoing work on VAI tool: moved regulatory data into own section, suppressed regulatory details from protein-coding consequence lines because they're in regulatory feature lines (#11461). Angie
• Ongoing work on GBiB including installation helpers for Windows and OSX (#11957). Max

Data changes:

• Created a Retroposed Genes track for hg38. Rachel
• Added MalaCards linkout from hgGene (#13311). Brian
• Added chains/nets to/from dp4 and droPer1 (and droPer1 selfChain). Hiram
• Started work on Gene Interactions (pubs) track (#13634). Max
• Completed work on Locus Reference Genome (LRG) track for hg19, hg38: handle multiple data source names and urls; substitute URLs that have moved (#13359). Angie
• Added COSMIC to optional annotations in VAI. Angie
• Completed new assembly browser for rat, rn6 (#13578). Hiram
• Completed new track DNaseI Master Sites from ENCODE/Analysis (#13230). Kate
• Ongoing work for ENCODE Regulation DNAseI Clusters track update to V3 (#13490). Kate
• Ongoing work on new assembly browser for D. melanogaster genome release 6 (#4049). Chin