v351

Code changes:

• Major enhancements to hgHubConnect to now show expanded search details, and provides direct links to matching tracks and assemblies (#13625). Jonathan
• New CGI, hgLinkIn, which translates external identifiers to assembly positions (#16668). Jonathan
• Further support for HGVS n. searches (NR_*:n.*) (#19423). Angie.
• Enhancement to genePredToFakePsl: merge contiguous exons that are split in genePred to represent ribosomal frame shift, but that need to be merged for proper PSL. Also fixed unsigned int underflow in corner case. Angie
• Minor makefile-tweaking and hgLogin cgiScriptDirUrl() change instead of "/cgi-bin/". Angie
• Enhancements for new hgGeneGraph CGI including adding it to the Tools Menu (#13634). Max
• Fixes for GBiB/GBiC hgMirror for bigGeneDataUrl and knownToTag (#19587). Max
• Fixes for hgSession/hgLogin where links on genome-euro/asia went to genome (#19632). Max
• Correcting a bug that had crept into lineFile.c that made it so that if used with udc, things could no longer read from a pipe. Jim
• Making a tabToHtml program that converts a tab-separated file to a HTML page with an embedded table. Jim
• Adding a little wrapper lib/uuid.c inc/uuid.h module to help work with universally unique identifiers, which have become quite common. Jim
• Setting up tagStorm format so that it can handle comma separated values. Jim
• Making tagStormJoinTab work on non-unique tags. Jim
• HCA: Building system for converting GEO and ArrayExpress metadata to TagStorm, massaging the tagStorm into an internally consistent format, and then exporting it in JSON format for the Human Cell Atlas (HCA). Jim
• CIRM: Implementing limit clause in tabQuery and tagStormQuery. Jim
• CIRM: Building a tagStormRenameVals utility to help cope with controlled vocabulary changes mostly. Jim
• CIRM:Refactoring tagStormToTab to optionally handle csv output for CIRM. Galt
• CIRM: Added .tsv support to cdwMakeValidFile. Galt
• CIRM: cdwWebBrowse: Added navigation first prev next last links. Also made it reset the page number back to 1 if anything changed such as: clear search button pressed, search changed, filters changed. Galt
• CIRM: Added csv file validator to cdwMakeValidFile. All rows must have same number of columns. Galt

Data changes:

• Work for the new Zebrafish assembly (#19459). Christopher
• Adding changes for new Quake expression track (#19517). Christopher
• Added chainNet hg38 for <---> equCab2 per user request (#19511). Hiram
• Updated sheep photograph for oviAri3 (#19237). Hiram
• Work on CRISPR script, still in progress (#19514). Hiram
• Building papAnu3/baboon browser for CIRM, chrM required and turns out there is a complete new assembly that should be used, but it doesn't have a chrM (#19660). Hiram
• Ensembl v89 build completed (#19526). Hiram