v389

Code changes:

• New feature for barChart tracks -- trackDb setting: barChartMaxHeight (#19872). Kate
• Extensions of recently added feature for composite tracks: trackDb setting, hideEmptySubtracks. This adds user configurability and support for a summary file to improve performance. Also, adds filter activated notice (#23365). Kate
• Adding new bottleneck behavior to hgGeneGraph, refs (#24240). Max
• Modified pslCheck to capture PSL parse errors and report them instead of failing. Also added option to act as a filter and not error exit on problems. Mark
• hgTables now provides selectors for resolution and normalization in Hi-C tracks (#18842). Jonathan
• Initial commit of a hicInfo command-line tool to provide basic information about a .hic file (#18842). Jonathan
• Initial commit of example Hi-C tracks on hg19 and hg38 (#24273). Jonathan
• Creating the first otto archive, for mastermind, (#24157). Max
• Bug fix to composite track labels -- filter activated, now included in label in dense mode. (#23365). Kate
• Bug fix to bigNarrowPeak visibility selection (support pack and squish). (#24249 ). Kate
• bigBedFind: support searchIndex in the search spec (not just trackDb) refs (#23283). Angie
• bigDbSnp.as, dbSnpDetails.as with utils dbSnpJsonToTab, checkBigDbSnp, script doBigDbSnp.pl refs (#23283). Angie
• Small hubCheck bug fixes (#18807). ChrisL
• First round of adding archiving commands to otto build scripts (#21825). ChrisL
• Optimize the javascript on hgHubConnect for drawing the search results faster (#23812). ChrisL
• Ongoing work on bigBed filters. Brian
• Fix bug in multiWigs that resulted in first track disappearing Brian
• Fixed default score filters on bigBeds with 9 or fewer fields Brian
• Correctly guarding protected tables in the hubApi (#24208). Hiram
• Platinum genome assembly hubs in QA (#21784). Hiram
• added support in hubApi for track types: bigBarChart, bigInteract, bigLolly, wigMaf, clonePos (#23589). Hiram
• CIRM Removed read_size column from field list as requested. fixes (#22990). Galt
• CIRM Removed mention of TabToSave from download page. More trouble to fix than it was worth. fixes (#22202). Galt

Data changes:

• Completed 3 tracks in new ENCODE Regulation supertrack for mouse mm10. Histone ChIP-seq, Open Chromatin by ATAC-seq, Chromatin State by chromHMM. These are now in QA (#23880). Kate
• gnomAD variants track for hg38. Now in QA (#21782). Kate
• LRG update (#24285). Angie
• Final touches to new mm10 and hg38 knownGenes. Brian
• Added crisprAll track for mm10 QA ready (#24296). Hiram