v283
- v283 Preview 1 - 22 April 2013
- v283 Preview 2 - 29 April 2013
- v283 Final - 6 May 2013
Code changes:
- Added support for HTTPS in hgSession (#10647). Galt
- Debugged CENTOS6 problems and new hgnfs1 machine (#9858). Hiram, Admins
- Allowed CGI timing function to be controlled via options in hg.conf file (#10611). Hiram
- Continued improvements to makefile system; destination binaries now depend upon their objects and the libraries (#9104, #10630). Hiram
- Ongoing work on Variant Annotation Integrator (#6152). Angie
- Ongoing work on Assembly Hubs (#8072). Brian
- Ongoing work on Gene Haplotype Alleles feature (#10653). Tim
- Clarified trackDb.doc for two settings: url2 and sortOrder. Tim
- Fixed wigColorBy bug hgTracks right-click update (#10512). Tim
- Fixed clipping error in anti-aliased lines that could cause crash (#10745). Brian
- Tolerate missing "freeze" field in assembly hubs. Brian
- Fixed bug in handling of right-click on a hub track. Brian
- Fixed bug in updating hubStatus table with longLabel. Brian
- Libified hub connection so VAI wouldn't duplicate code. Brian
- Fixed a buffer flow problem which caused a crash for bigWig custom tracks (#10686). Brian
- Fixed some problems with spaces in labels in bigBeds. Brian
- Sped up bigBed's handling of long records. Brian
- Correctly order assembly hub databases using orderKey. Brian
- Properly set UDC cache directory in genome graphs and hgHubConnect. Brian
- Fixed link from gene details page to Interpro. Brian
- Added a new option to gtfToGenePred: ignoreGroupsWithoutExons which skips groups containing no exons. Mark
- Added new library functions: twoBitTotalSizeNoN, netWaitForData, and freeSpaceOnFileSystem. Jim
- Several improvements to autoSql: You can now specify indexes and auto_increment in the .as file. A new command line option to set empty string and 0 for default values, which is often needed with newer versions of MySQL. Fixed some obscure bugs that had been around for ages including a bad interaction between the -withNull option and the sets/enums, and another bug where the code to load database given C structure didn't work for blob fields. Also added -withBin option to add a chromosome-range bin index. Put in a list of fields known at compile time as a comma separated string. Jim
Data changes:
- Ensembl Genes v71 track for many assemblies (#10636). Hiram
- Created chain/nets to/from dog (canFam3) and chimp (panTro4) (#10712). Hiram
- COSMIC track (v64) is now automatically released (#10158). Hiram
- Rebuilt drBlastTab table for several assemblies to match Ensembl Genes v70 (#10464). Chin
- Added description field for hg19 ensemblLift table (#10496). Chin
- Finished ENCODE Uniform TFBS track (#10042). Kate
- Ongoing work on ENCODE Regulation Transcription Factor ChIP (TFBS Clusters) track update (#10097). Kate
- Ongoing work on Retroposed Genes track for hg19, mm10 (#3867, #1513). Rachel