- v388 Preview 1 - 9 September 2019
- v388 Preview 2 - 16 September 2019
- v388 Final - 23 September 2019
Code changes:
- Support multiple hubUrl's on URLs (#16200). Brian
- Allow track hubs to attach to assembly hubs (#16200). Brian
- Add "group auto-scale" to wiggle controls (#3420). Brian
- Interact multi-region link feature (on details page) ready for
prime-time. Fixes cross-chrom issues, adds specification of custom
region padding to trackDb setting, constructs custom track showing
custom regions (#24037). Kate
- Adding the new bottleneck rules also to hgGeneGraph (#24094). Max
- Addition of earlyBotCheck() function to more CGIs (#23217): Hiram
- hgCustom
- hgTables
- hgGateway
- Minor UI improvements to multi-region, prompted by interact
multi-region feature: adds regions size to region list in pop-up, style
position box when in MR mode (#24037). Kate
- Extend labelOnFeature trackDb setting; add 'noDense' modifier so
labels do not appear in dense mode (consistent with dense mode w/o this
setting). Used by new Chromatin State track (#23880). Kate
- Added support for Hi-C tracks in track hubs and Hi-C composite tracks (#22316). Jonathan
- hgSession re-saving corner case bug fixes: Angie
- don't lose the session when a re-saving errAbort is encountered (#24119).
- don't errAbort when a previous re-save has timed out, leaving a partial file (#24121).
- don't SEGV when a wiggle table has 0 rows.
- don't trimSpaces(sessionName) when re-saving (some old sessions have spaces) (#24124).
- remove redundant 'use' and 'delete' buttons from form to change session details (#24133).
- Moving towards next generation otto-archiving, starting with mastermind (#24157). Max
- Remove hgGene links to chimerax application (#22953). ChrisL
- Fixing a nested directory bug in hubClone (reported by lrnassar). ChrisL
- JSON API enhancements:
- Fix hubApi to manage big* files correctly for schema output (#23589). Hiram
- Now hubApi correctly checks chrom size for data output with coordinates (#24089). Hiram
- Now hubApi places list tracks for database genome in JSON container (#24127). Hiram
- Now correct hubApi list chromosomes for big* track from database table URL (#23589). Hiram
- Work that may be more generally useful for loading relational databases, including making foreign keys connections. Jim
Data changes:
- The VGP hub became complete https://hgdownload.soe.ucsc.edu/hubs/VGP/ (#23734). Hiram
- Finish Mouse ENCODE Regulation supertrack (3 tracks) for mm10. Tracks
are: Open Chromatin (66 ATAC-seq experiments), Histone Modifications
(563 ChIP-seq experiments), Chromatin State (66 ChromHMM datasets). Now
in QA (#23880). Kate
- Assistance in import of GENCODE data. MarkD
- New mm10 UCSC GENCODE genes VM23 (#24087). Brian
- New hg38 UCSC GENCODE genes V32 (#24032). Brian