v349

Code changes:

• Added ability for user to paste a custom BED region into the multi-region dialog box instead of having to provide a URL to an online server (#17538). Galt
• Make density graphs use exons instead of the length of the whole feature (#19300). Brian
• New CGI hgGeneGraph: for protein interactions track viewer coming for hg19 and hg38 (#13634). Max
• Final work on barChart and bigBarChart tracks, for announcement with v349. Added custom tracks and table browser support. Affected CGIs and tools: hgTracks, hgc, hgTrackUi, hgCustom, hgTables, hubCheck (#18736). Kate
• Ongoing work on custom dynamic composites (#11630). Brian
• Added a new hg.conf option, login.relativeLink for firewalled genome browsers. Max
• HGVS term search: map transcript bases deleted from the reference genome to genome indel point [e.g. our hg38 default locus, ABO -- reference genome is missing a base from the transcript, but it is quite common and is how we get the O blood type.] (#19396). Angie
• HGVS term search: fixed off-by-one for negative coords (#19396). Angie
• Fix default track colors on bigGenePred type (#19341). Brian
• Updated the script expMatrixToBarchartBed and infrastructure to make barChart bed files (#19155). Christopher
• Added new tools (expMatrixToBarchartBed and bedJoinTabOffset) to User Apps package (#18736). Kate
• Adding support for hgSession to find ImageMagick convert on GBIB (#19296). Jonathan
• hgVai: do not show loading... image/message when output is going to a local file (#19305). Angie
• hgVai: use latest snpNNN that is in trackDb, not just latest database table (#19272). Angie
• Background work on VCF to proper transcript HGVS for VAI output and background pipeline work on snp150. Angie
• Working on a little prototype for adding more context to return result on a trix search. Jim
• Added bedJoinTabOffset for GTEx (#18736). Max
• Added markDownToHtml, converts markdown -> gb static html page (#13634). Max
• Fix for an old GBiC bug on Redhat (#19380). Max
• Fix for crash in hubCrawl if descriptionUrl cannot be opened (#19356). Brian
• Make rangeTree functions thread safe (#19385). Brian
• Added code to preserve the trash file in saved sessions. Helped staff upgrade trash cleaners/preservers (#17538). Galt
• Setup refreshNamedSessionCustomTracks to save new multi region files from Galt and new hgComposite trash files from Brian when saved in named sessions (#17358). Hiram
• CIRM: Fixed some minor CSP issues in cdw for CIRM. Libraries needed to be explicitly allowed in cheapcgi.c. A redirecting URL needed to be replaced with the actual final URL. Advised Jim on adding a parameter to a tagStorm utility so that it can emit a nonce with the html page output with javascript for expanding/contracting nodes. Galt
• CIRM: Making CIRM web site work with new CSP protections. Jim

Data changes:

• Updated the COSMIC track for hg19 and hg38 (#14461). Christopher
• Fix for CRISPR track for Hiram and Regeneron. Max
• New criGriChoV1 genome browser, to remain hidden for six months on hgwdev-demo8.soe.ucsc.edu (#19228). Hiram
• New xenTro9 with 11-way multiz with xenLae2 and chrPic2 browsers (#19151). Hiram
• Reset default visibilities for both criGri1 and criGriChoV1 browsers (#19228). Hiram