v173-final - 3 Jan. 2008    (Pairings)

Code changes:

• Use same graph color for chromGraphTrack.c as in hgGenome. (Andy)
• Ongoing work on snp128. (Angie)
• In hgTables,cChanged identifierHash to take a db arg in addition to table, so it can form db.table to match curTable when necessary. (Angie)
• Replaced some hardcoded POSTs with cart var formMethod in hgTables/filterFields.c. (Angie)
• Bug fix in hgTracks/wigMafTrack.c for blank alignments in regions using codon translation. (Brian)
• Bug fix in lib/maf.c where blue bars in browser were being incorrectly drawn. (Brian)
• Added options to mouseStuff/chainFilter to filter out chains with large gaps. (Craig)
• Changed utils/faFilter to allow multiple patterns to be filtered, the same as multiple -name options. (Craig)
• Ongoing GSID work. (Fan)
• Fixed problems with modBase images in hgGene. (Fan)
• Added links for Seattle SNPs PGA genes and geneTest links on hgGenes page. (Fan)
• Onoging work on ENCODE submission pipeline. (Galt)
• Mods to hgAutomate.pm and doBlastzChainNet.pl automation scripts. (Hiram)
• Changed ratStuff/mafFrags so that database doesn't have to be first item in org list. (Jim)
• Work on ENCODE validation scripts. (Kate)
• Fixed link on CCDS genes within PAR by including chromosome in selection, fix link to CCDS site to function when a CCDS is deleted in a new assembly but still valid in older one. (Mark)

Data changes:

• Created Affy Transcriptome super-track. (Andy)
• Added notes to rheMac2 docs about the omission of simpleRepeat filtering -> trfMaskCrhom, which led to overmasking (reported by user). (Angie)
• Added Seattle SNPs PGA genes and geneTests. (Fan)
• Added SGP and geneid tracks to several assemblies. (Hiram)
• Work on calJac1, ponAbe2 browsers. (Hiram)
• Updated procedure for mafFrags use to make upstream maf files from multiple alignment table (several assemblies). (Hiram)
• Build swap chains for several assembly pairs. (Mark)
• Updated hg17, hg18, mm8, mm9 CCDS tables. (Mark)