v176-preview - 12 Feb. 2008    (Pairings)

Code changes:

• Replaced several older SNP-masking programs with versions that work on input files (not db) and include FASTA headers in output. (Angie)
• Additions to snp/snpLoad/snpNcbiToUcsc.c to support mouse SNPs. (Angie)
• Mods to hgc.c -- Added display of more ortho allele info for snp125 tracks; also wrapped a table around both reference and ortho alleles so they line up for easy comparison, added better error-reporting for incorrect coords passed to SNP details from manually constructed links. (Angie)
• Updates to browser build automation files, adding Ensembl gene automation. (Angie, Hiram)
• Modified utils/splitFileByColumn -- when looking for first . for file suffix, ignore directory names in the path (like ..). (Angie)
• Minor tweaks to GSID pages. (Fan)
• Ongoing work on instinct. (Fan, Jing, Ting)
• Ongoing work on ENCODE submission pipeline. (Galt)
• Mod to hgc.c -- do not try to predict Ensembl genes if there is no protein for them; they are most likely non-coding. (Hiram)
• Work on liftAcross. (Hiram)
• Ongoing work on ENCODE validator. (Kate)
• Work on UCSC Genes update. (Jim)
• Replaced unused genePred ID column with score column. (Mark)
• Added geneName and transcriptName to gff object. (Mark)
• Added code to ratStuff/mafToAnc/ for finding alignment anchors in an argument maf file. (Rico)
• Fixed memory leak in lib/linefile.c, added lib/anc.c. (Rico)

Data changes:

• Added resequencing trace experimental track to hg18. (Andy)
• Work on mm9 snp128. (Angie)
• Work on phastCons for hg18 multizPrimate. (Brian)
• Ongoing work on petMar1 -- genome rebuilt as scaffolds instead of chrUn. (Hiram)
• CCDS update in hg17, hg18, mm8, mm9. (Mark)
• Added new hg18 expression difference data track and expression time difference map (instinct). (Ting)