v189-preview - 12 Aug 2008    (Pairings)

Code changes:

• Changed several hgwdev commands to use /data/tmp instead of scratch/tmp. (Angie)
• Added amino acide properties to display in lib/pgSnp.c. (Belinda)
• Added getPFamDomainList() -- use instead of getDomainList for Pfam to work around the unique defintion of pFamDesc table. (Fan)
• Modified lib/wikiTrack.c to allow creation of the table on first use when it doesn't exist. (Hiram)
• Updated EnsGene automation scripts. (Hiram)
• Reworked protein/hgBioCyc1/kgBioCyc1.c. (Jim)
• Fixed super-track bug in hgTrackDb.c. (Kate)
• Ongoing work on ENCODE loader, validator, and automation. (Larry)
• Removed hgTracks/bedGraph.c/bedGraphTotalHeight; use wigTotalHeight instead to fix problem with disappearing zero values in bedGraphs. (Larry)
• Performance mods to hgExpDistance. (Lee)
• Added read/write to genomeRangeTree and rangeTree. (Mike)
• Added support for retroGene track, support for psl tracks and codon coloring for retrogenes. (Robert)
• Fix for hgTrackUi supertrack UI bug that failed to show subtracks that are composites. (Tim)
• Ongoing work on instinct. (Zack, Chris, Steve)

Data changes:

• Mapped clone IDs from Kidd Eichler track to NCBI clone accessions and/or end read trace names. (Angie)
• Reloaded snp128 and snp129 with new auto-generated .sql that includes enum and set values only if they appear in the data, so TB filter doesn't show misleading choices. Swapped genomic/cDNA in dbSNP fasta headers for snp129. Updated hg17 DGV to v5 and added kiddEichlerToNcbi IDD xref table for HGSV. (Angie)
• Fixed up chrom names for taeGut1. (Brian)
• Ongoing work on 2X alignments. (Brian)
• Work on Illumina 1M track for hg18, updated hg18 uniGene track. (Fan)
• Generated bosTau3 and bosTau4 self blastz (mailing list request). (Hiram)
• Started Ensembl50 update. (Hiram)
• Updated hg18 bioCyc pathways. (Jim)
• Ongoing work on nemVec1. (Kord)
• Added retrogene track. (Robert)