v401

Code changes:

• New vcfPhasedTrio changes (#18846) (#25582). Christopher
  • Add drag re-order of trios
  • Add button for quick ordering of trios
  • Make vcfPhasedTrio an allowed track hub type
  • highlight child lane in yellow even when child is on top or bottom of trio
  • Shade child alleles if there is potentially inconsistent transmission from the parent
• VCF tracks: new option to color haplotype display by variant's effect on gene (#25870). Angie
• Tree-parsing speedup for large tree files w/tens of thousands of nodes. Angie
• Added warning when a dbSnp table is selected in the table browser (#25775). Max
• Fixed genePredToGtf to correctly number exons on the negative strand (#25379). Hiram
• Fixed bug in hubApi for whole genome data fetch (#25840). Hiram
• Fixed old bug in doBlastzChainNet.pl to correctly get *.net.gz file into md5sum.txt (#25279). Hiram
• Ongoing work on making knownGene tables live in their own database. Brian
• Changed gitFiles program to check to see if the current directory is in a git repository. Brian
• Added GENCODE section to hgGene. Brian
• Added noGenomeReason trackDb statement for omim and Crispr tracks (#25428). Max

Data changes:

• Updated Nextstrain tracks to include their new clade designations in addition to old (#25782). Angie
• Lab-associated mutations (from manuscript submitted by Russ et al.) (#25804). Angie
• Added panPan3/bonobo genome browser (#25720). Hiram
• Added canFam4/german shepard genome browser (#25279). Hiram
• Added chainNet droSim2 vs. droSec1 per user request (#25823). Hiram
• Correctly cited Bob Harris in lastz chain/net documentation. Hiram
• Ongoing work on gencodeV35 as ONLY Gencode track. Brian
• Added liftOver chain tracks to hg19 and hg38 (#24449). Max
• RAPID primers wuhCor1 track (#25847). Max
• Converting uniProt to bigGenePred format, for now only on wuhCor1 (#25192). Max