v337

Code changes:

• Make hgSession/hgLogin use HTTPS for hgLogin, unless disabled in hg.conf with login.https=off (#17778). Angie
• Fix to remove artificial limit on number of sessions listed in Public Sessions (#17825). Jonathan
• Enhance hgTracks to draw multiple highlights from the cart variable via URL not UI (#14951). Max
• Fix for the ${ and $} variables to mean start and end location of clicked item (#17785). Max
• Fix track hub problem where tracks in composites were not sorted in initial display (#17786). Brian
• Enhance track hub pennantIcon to take a URL (#17787). Brian
• Enhance speed of display of metadata on composite hgTrackUi page (#17790). Brian
• Fix track hub composite hgTrackUi page problem when there was only one experiment (#17795). Brian
• Fix bug involving strand and for "get alignment in window" for bigPsl format (#17829). Brian
• Fix bug in bigBed loading involving SQL calls. Brian
• Add script to merge several RNA-seq matrices into a bigger one. Max
• On details page for SNPs add a missing link to SO term intergenic_variant (#17209). Angie
• Fix hgIntegrator behavior around bin column for tables with bin in autoSql (#17748). Angie
• Enhance hgGateway (hDbForTaxon) to guard against extra rows in dbDb for hgwdev-only dbs (#17886). Angie
• Enhance SNP track pipeline script to check for chrom names with and without version numbers (#16846). Jonathan.
• Fix to gff3ToGenePred around encoding of +1 and -1 translational frame shifts. Mark
• Work on assembly hub creation scripts (#13553). Hiram
• CIRM: Add Download all button to data warehouse (Browse - files). (Max)
• CIRM Add RNA-seq data summary plotting html to data warehouse. (Max)
• CIRM: cdwCheckDataset -add wrangler who submitted dataset; cdwSubmit.c -add wrangler column and added in an automatic backup on submits; cdwFlowCharts library changes (#17334,#17187). Chris
• CIRM: cdwMakePairedEndQa, cdwLib.c and cdwMakeContaminationQa -put in poly trimmer for poly A and poly T reads after the sub samples are taken but before they are aligned (#17334). Chris

Data changes:

• Recomputed snp147* tables with fixed functional annotations for non-coding indels (#17209). Angie
• For snp* since 138 corrected outdated trackDb settings chimpDb and macaqueDb (#17209). Angie
• Added DGV 2016 update (#17351). Angie
• Added LRG update (#13359). Angie
• Adding of steps towards CRISPR tracks for most model organisms (#17235). Max
• Documentation for cow bosTau8 SNP track - dbSNP 148 (#16846). Jonathan
• Change to only do Genbank data alignments on assemblies on beta, and data changes to gbStatus. Brian
• Added panTro5 assembly (#17817). Hiram
• Added gorGor5 assembly (#17580). Hiram
• Added ensGene v85 (#17863). Hiram