v316

Code changes:

• Ongoing work on GBiB: allow bigFile tracks without tables (#15059); Fixed a problem where a GBiB update was overwriting local hg.conf.local file (#15254). Max
• Added new code to build mafSnp tables for conservation tracks (#14970). Brian
• Added option to enable mafSnp mode if snpTable is present (#14970). Brian
• Added tables to knownGene to keep track of exon frames (#14639). Brian
• Fixed bug in BAM display to ignore mate-pairs that are on different chroms (#15250). Brian
• Ongoing work on jsonToTagStorm: converts a .json file to a tagStorm file. Chris
• Ongoing work on tagStormToJson: converts a tagStorm file into a .json file. Chris
• Wrote code to create a colored d3RadialDendrogram. Uses D3 and .json to generate the graph. Chris
• Fixes to Table Browser: fixed recently introduced bug that broke MAF output (#15117); fixed filterFields for bigDataUrl-only tracks (#14379, #15059). Angie
• Ongoing work on Data Integrator (previously referred to as Annotation Integrator), hgIntegrator including: CSS styling more consistent with other CGIs; fixed loss of some data values in regulatory data; added column descriptions in Choose Fields popup; added Data Integrator to Tools menu on non-public hosts on which hgIntegrator has been built; added support for pasted/uploaded user regions (#14579, #11461). Angie
• Changed links from main browser to genome-store from POST to GET (#15251). Jonathan
• Changed grp.sql to drop the grp table before attempting to create a new one. Mark
• Changed the code to generate an error rather than SEGV if genomeClade is not found due to misconfigured hgcentral. Mark
• Allow for hgloadBed to load zero-length BEDs at the beginning of a chromosome. Mark
• Improve error message from gff3ToGenePred to make it easier to determine where bad GFF3 annotations created an invalid genePred. Mark
• Fixed lavToPsl command to manage new problems in lastz v66 (#12502). Hiram
• Fixed bug in click-through on micMur1 chain/nets (#15112). Hiram

Data changes:

• UCSC Genes on hg38 based solely on Gencode gene models (#14639). Brian
• Added MAF-SNP display to 20-species Conservation track on hg38 (#14970). Brian
• Added MAF-SNP display to 20-species Conservation track on tarSyr2 (#15112). Brian
• Created 1000 Genomes Phase 3 track for (#14325). Angie
• Created 100-species Conservation track for hg38 (#14560). Hiram
• Added GRCh's Patch 3 to hg38 (#15413). Hiram
• New assembly browser for Mouse Lemur, micMur2 (#15292). Hiram