v467

Code changes:

• Removed some of the text below the hgTracks image. (#26325). Max
• Made some tooltips have longer delays than others and removed some of the less helpful tooltips (#33540). Chris
• hgc page for BAM: removed the "English" CIGAR text and added a new legend for normal cigar string (#33292). Max
• Added endpoint to the API: genarkGenomes - to list the GenArk genome assemblies or test if one exists, remains to be documented. Hiram
• Added support in the API for bigChain, bigMaf and bigDbSnp track types, remains to be documented (#24430). Hiram
• Added new API function -revComp to the get sequence complement (reverse)(#26691). Hiram.
• bigBedInfo now outputs the no. of defined fields. Max
• Added hg.conf option to load a mirror-specific .js file (for china mirror). Max
• Made the hgTracks basic tutorial on by default and document the hg.conf parameter (#33992). Chris
• hg.conf option to switch on itemRgb by default (#28498). Max
• hg.conf option to remove the dink left/right buttons under the image (#26325). Max
• Added option for overlapSelect statistics output to have a TSV header on output. Mark
• Added chainToBigChain command. Mark
• Added pslToChain -fixStrand option to correct negative target strands rather than abort or ignore psl. Mark
• Fixed decoding of chain scores in hgc, which is a double in the data structures; it still displays as an int in hgc. Mark
• errAbort instead of SEGV when bigPsl alignment table is not found. Unsure why this happened, but at least this removes the white screen of death. Included a note about periods in track names that can cause failure. Mark
• Include track name in some of the filter error messages so we can have a clue about what to fix. Mark
• lib/vcf.c: fix bug in parsing of END keyword when not defined in the VCF header. Angie
• Continuous GenArk process improvements (#29545). Hiram

Data changes:

• gnomAD missense and pli v4.1 tracks ready for QA. Chris
• NMD decorators on knownGene for hg38 (#33737). Max
• Improvements to wuhCor1 big tree build process. Angie.
• Continuous GenArk updates and liftOver file generation (#29545). Hiram