v321
- v321 Preview 1 - 10 Aug 2015
- v321 Preview 2 - 17 Aug 2015
- v321 Final - 24 Aug 2015
Code changes:
- Taught hgVai about diffs between wgEncodeRegDnaseClusteredV3 for hg18 and wgEncodeRegDnaseClustered for hg38. Angie
- Fixed a typo in wikiLink lib that caused hgSession 'sign out' to act like 'sign in' (#15217). Angie
- Fixed the anno* libs to prevent region-average wiggle values from being split into multiple region averages (#15834). Angie
- Fixed the annoFormatTab lib to start header with # even when all fields of first table are deselected (unlikely but could happen). Angie
- Fixed the annoGrateWig lib to use isnan because comparing to NAN does not work. Angie
- Fixed annoStreamBigWig lib: don't stop after chr1 in genome-wide query (#15813). Angie
- Fixed annoStreamDb lib corner case that caused loss of last item when all items are in coarse bins (#15867). Angie
- Exclude custom MAF tracks (not just wigMaf) from the Data Integrator (#15857). Angie
- Queue up requests in cart.js lib so that all commands can be sent with identical cart variable settings when the dust settles - now requires explicit flush. Angie
- Require the Data Integrator to deal with some hgwdev inconveniences: extra whitespace in dbDb entries in flux, databases that are active in dbDb but don't have trackDb tables, tweaked sql definitions that are hard to match back up with autoSql, more unsorted tables. Angie
- Added several tools to the Send To menu (#15113). Max
- Allow empty name fields in bigBed files (#15780). Max
- Turn on the Short Match track if anything is typed into the "motif" section of the hgTrackUi page (#15871). Max
- Added new program tagStormRenameTags which takes a tagStorm file and replaces existing tag names with tag names we want based on a 2-column input file. Steve
- Fixed axtChain command to fail more gracefully with useful error message when users mix up the command line arguments or use incompatible sequence files vs. alignment files (#15899). Hiram
- Added link on gene details page to GTEx (Genotype Tissue Expression) for all human assemblies (#15649). Kate
- Added SSL Support to hg.conf, hg/lib/jksql.c and to the hgsql-and-family functions (#15751). Galt
- Added SSL documentation to src/product/README.mysql.setup. Galt
- Added HGDB_PROF env setting to override default profile. Galt
- Added -profile command-line option to hgsql utility. Galt
- Removed unused and obsolete utilities hgsqlLocal and hgsqldumpLocal. Galt
- Check MySQL version at compile time (#15835). Galt
- Fixed bug with PSL to genePred frame correction when there is target deletion (#15803). Mark
- Fixed bug converting GFF3 alignments to PSL when alignments start or end with indels. Mark
- Added pslClone utility. Mark
- Converted macros to access PSL strands to inline functions to improve code reliability. Mark
- Started work to support a new data type: bigPsl (#14241). Brian
- Increased buffer length for host name and passwords (URL) in network layer. Brian
- Added a new utility, hubCrawl, to produce the strings used in the hub search. Brian
- Fixed right-click menu to support "open config in new window" (#15820). Brian
- Allow more than 1024 blocks in a bigBed (#14241). Brian
Data changes:
- Disabled pop-up configurations for Exome Aggregation Consortium (ExAC) track because old JS code mangles cart variables that use multishad (#14379, #15873). Angie
- Fixed typo in wgEncodeGencode*View2Way. Angie
- Fixed another case of 'bed N .' that should be 'bed N +' (#15610). Angie
- Loaded CNV Developmental Delay track, hg38 (#9391). Steve
- Updated all assemblies to Ensembl Genes v81. This includes new name information gleaned from the Ensembl GTF files (#15796). Hiram
- Created BAC Ends track for hg38 (#13713). Hiram
- Created microsat track for all assemblies (#15398). Hiram
- Started work on nematode 26-species alignment for new C. elegans browser: ce11 (#15209). Hiram
- Created STS Map track for hg38 (#15524). Hiram
- Changed short and long labels for GENCODE Genes, hg38 (#14639). Brian
- Lifted fishClones track from hg19 to hg38 (#15522). Chris
- Lifted fosEndPairs track from hg19 to hg38 (#15523). Chris
- Lifted IKMC track from hg19 to hg38 for the newly-created non-coding RNA super track (#11694). Chris