v335
- v335 Preview 19 - 25 June 2016
- v335 Preview 26 - 2 July 2016
- v335 Final 4 July 2016
Code changes:
- Added cram auto-detect so no track line is needed in hgCustom (#14717). Max
- Turned on use of new trf binary v4.09 for simpleRepeats in the automatic script doSimpleRepeat.pl (#17580). Hiram
- Fixup chain/net coloring scheme for WGS contig assemblies to use the same 10 color palette as the snake track display does, this function used to reuse the chromosome color scheme which could be misleading (#17580). Hiram
- Improvements to support new bigMaf, bigPsl, bigChain and bigGenePred formats (#17325). Brian
- Added next/prev item support to longTabix support. Brian
- Ongoing work around the arrangement of Genbank tables. Brian
- hgVai fix to handle new hgFixed location of refSeqStatus for RefGene txStatus info (#17597). Angie
- cartTrackDb access control (hgTables, hgIntegrator) to fix side-effect of noGenome support that was failing for assembly hubs (#17588). Angie
- hgMenubar can optionally process a file other than inc/globalNavBar.inc (for new footer). Angie
- hgGenome Graphs fix to allow SNP queries (#16983). Galt
- Improved hgTablesTest robot to allow randomizing the track and table lists, along with a -noShuffle option for more control (#17499). Galt
- Changed hgTracks mulit-region customUrl mode to act like exon/gene-mostly virt modes instead of trying to switch to a full-virt-chrom view which may be too large (#17617). Galt
- Fixed a problem with the maxIntron option in BLAT when a non-default value is used in a protein query (#17624). Galt
- Keyboard shortcuts added to hgTracks to get to hgPublicSessions (#17469). Jonathan
- Assorted fixes and updates for otto track pipelines (#14465). Jonathan
- CIRM: Ongoing work on CIRM UI and DW. Jim
- CIRM: Changes to address bugs, fix variable names, move files and enhance flow chart
regarding cdwFlowCharts.c, cdwDumpManiFiles, cdwCheckValidation, and cdwCheckDataset (#17187 #17619 #17100 and #16113). Chris
Data changes:
- Released new home page design (#17470). Angie
- Lastz/chain/net run per user request panTro4 and hg18 to gorGor4 (#16414) Hiram
- Gencode Genes for hg38 (#10968) Brian
- Re-make of refGene alignment for hg19 multiz100way (#17598). Brian
- Make Pfam track smarter about using minimum scores from HMM (#17531). Brian
- Minor updates to GTEx track documentation. Kate
- Fixed html errors found by hgTablesTest (#17499). Galt
- Small changes of the order of fields for clinvar track. Max
- CRAM documentation (#14717). Jonathan