v342

Code changes:

• New CGI that provides dynamic highlighting and selection of the 53 GTEx tissues on a human body illustration ("GTEx Body MAP"). The new CGI (hgGtexTrackSettings) replaces the previous GTEx Gene track configuration page (#17369). Kate.
• Addition of new trackDb setting bigDataIndex for vcfTabix and bam files to allow indexed data file to exist at an alternate URL (#18420). Max
• Addition of keyboard shortcuts 1-5 to zoom to range span and note about "?" to see list of keyboard shortcuts (#18367). Max
• Codon numbering is now on by default for GenePred-type tracks (you still have to zoom-in enough to see them) (15459). Jonathan
• Addition of a simple command line wrapper script for hgVai (#12216). Angie
• Addition of hg.conf controlled ability to output BLAT results as a custom track (#2811). Brian
• Fix for a bug in "View details of alignment" in current BLAT results track (#2811). Brian
• Added further support for tagStorm files in track hubs (#18183). Brian
• Improved tagStormInfo to include more information with the -counts option. Jim
• Add support for protein psls in bigPsl (#2811). Brian
• Fixed problem with errors in HAL snakes showing in half height tracks (#15596). Brian
• Introduced required group "map" to always exist and contain Base Position, Short Match, and Restriction Enzymes to enhance assembly hub organization (#16170). Brian
• Enabling allowing hub.txt, genomes.txt, and trackDb.txt to coexist in a single file for hubs (#18450). Max
• Some small fixes for GBIC. Max
• Support for split tables to annoStreamDb (#18397). Angie
• Addition of -lz and -lm options to all kent utils link commands to fix problems of when these are needed (#18336). Hiram
• Experimental work with making hal snake hgc clicks function better (#13553). Hiram
• Addition of bam to psl test file for the bamToPsl command (#13673). Hiram
• Addition of geneType and transcriptType to gtfToGenePred info output file. Mark
• Fix for converted hgTables resource output exceeded warnings to errAbort to avoid a duplicate header problem (#18300). Galt.
• Changefor link on Gene Details page to "Protein FASTA" to say "Other Species FASTA" (#18443). Brian
• hgTracks no longer crashes when trying to display certain mRNAs (18369) Jonathan
• New QA script to keep track of Public Hub emails, src/utils/qa/getPubHubContact.sh Matt
• CIRM: work to get browser custom track on CIRM data files to work with increased security. Jim
• CIRM: added support for png files; made .jpg and .pdf file links display in browser rather than download. Jim
• CIRM: added support for comma separated value (.csv) output of metadata query results. Jim
• CIRM: added a tag storm tree link to dataset page. Jim
• CIRM: Made tagStormToHtml which converts a tagStorm file (including trackDb files) to a collapsable hierarchical list in a web page. Jim
• CIRM: Baldwin lab summary pages part 1 and new Seurat support. Max
• CIRM: cdwManiFastqToKallisto: updating static file links and fixing a bug Jim noticed during a code review (#17630). Chris
• CIRM: cdwWebBrowse: updating and fixing some small bugs with the analysis:download query, added in a static image that links to a joint data set page to the home (#17870). Chris
• CIRM: cdwGetMetadataAsFile: adding in a function to incorporate user permissions (refs #18448). Chris

Data changes:

• ncbiRefSeqOther track converted from genePred to bed12 to avoid problem of trying to display non-gene annotations in a gene track (#13673). Hiram
• Clinvar track otto update for new format. Max