v330
- v330 Preview 1 - 7 March 2016
- v330 Preview 2 - 14 March 2016
- v330 Final - 21 March 2016
Code changes:
- Created automated script to fetch CRAM reference sequences in conjunction with hgTracks (#14717). Jonathan
- Updated parsing of GWAS data: new file format on their end, better character set translation on ours (#16925). Jonathan
- Changes to processing and display of OMIM data, including better handling of variants (#16796). Jonathan
- Added -defaultCdsStatusToUnknown option to gff3ToGenePred to default the CDS status to unknown rather than complete if there are start/stop codons annotations are not used. Mark
- Clarified mouse-over message on hgTracks image to more clearly explain that by pressing the double-headed arrow, you will move to the Next/Previous Exon Edge (#16505). Bob
- Replaced simple literal NOSQLINJ in string with the #define NOSQLINJ so the compiler will catch misspellings. Galt
- Fixed crash in custom tracks of type big* when user pressed nextItem (#16982). Galt
- Formatted bigBed extra fields as a table on hgc page (#14486). Max
- Added three new trackDb statements to fine-tune extra fields display on hgc: sepFields, skipEmptyFields and skipFields (#14486). Max
- Fixed a problem with SIG_PIPE in our https connection handling (#16872). Galt
- Fixed hgc position for multi-region modes with multiple different chromosomes on the screen, such as custom regions by url mode or alternate-haplotype mode (#16975). Galt
- Ongoing work on CIRM tools, data warehouse, and dendograms (#16216, #16341, #16244, and others). Chris, Max, Jim
- Fixed a problem with chain lines disappearing when zoomed way in (#15209). Brian
- Fixed a bug in outputting sequence in the table browser for refSeq table (#13673). Brian
- Set udcCacheDir setting in hgApi to enable metadata display. Brian
- Reset build variables to build user applications with SSL turned on (#16872). Hiram
- Added new function to common.c, isSymbolString(char *s); Return TRUE if s can be used as a symbol in the C language. Jim
- Libified code to find the latest snpNNN table, to avoid hardcoding version numbers (#16777). Angie
Data changes:
- Ongoing work on GTEx V6 gene tissue expression data and display, hg19 and hg38 (#15645). Kate
- Created several liftOver files to fulfill user requests (#16879). Hiram
- Created cloneEnds track for mm10 (#10083). Hiram
- Created GENCODE Genes VM9 for mm10 (#17007). Mark
- Created GENCODE Genes V24lift37, a lift from hg38 down to hg19. Mark
- Reverted the color scheme for the cell lines in the ENCODE Layered H3K27Ac track in hg38 and added a radial dendrogram image (#16844). Chris
- Final touches for FISH Clones track lifted from hg19 to hg38 (#15522). Chris
- Completed track from the Lens PatSeq Patent Document Database, hg19 mm10 (#14486). Max
- Fixed a problem with wormbase genes on ce11 (#15209). Brian
- Turned off intronEst track in hg19 by default. Brian
- Reran v146 SNP pipeline on hg19 after a problem was found. Ran v146 SNP pipeline on hg38 (#16777). Angie
- Corrected tgpPhase3 filenames for chrX and chrY (#16910). Angie