v383

Code changes:

• For API order data return by chromStart to allow fetching all track data with maxItemLimit interference (#18869). Hiram
• For API indicate parent of parent when two levels deep and trackLeavesOnly (#18869). Hiram
• Preparations for the ottomatization of the mastermind track, no redmine yet. Max
• Removed fixed limit on the number of block in pslToBigPsl. Mark
• Output total number of aligned bases in pslStats -overallStats. Mark
• hubCheck improvements - warn about incorrect tag=val pairs in subtrack subgroups line and warn about subtracks missing sortOrder subgroups, (#13428). ChrisL
• Fix bug in hgTrackUi where page was crashing when subtracks had missing subgroups required by a previous sortOrder definition, (#23556). ChrisL
• Added a fix from Daniel Zerbino to bigBed support that fixes a bug in very large file support. Brian
• Added code to postscript support for unfilled circles. Brian
• Added support in the lm routines to pass in a shared memory segment. Brian
• Ongoing work on trackDb caching with shared memory. Brian
• Sort hgHubConnect hub lists by short label. Brian
• When looking for a BAM index, try replacing .bam with .bai if just adding .bai to the end did not work. Brian
• Added scripts to re-save user sessions to get all session customTrash tables moved to customData- databases, and replace all cart references to trash symlinks with actual userdata locations. (#22440). Angie
• hubApi: support itemCount for big- tracks whose files are named in db tables not bigDataUrl, and for BAM and VCF+tabix tracks if their indices include item counts (#18869). Angie

Data changes:

• Finalize track configuration for imminent release of first ENCODE 3 (#21139). Kate
• Regulation tracks (Transcription Factor Binding Site ChIP-seq and Clusters) (#23243). Kate
• Many html pages fixed for problems found with htmlCheck. Galt
• Ongoing work on GDC Cancer track (#22742) Brian