v178-final - 18 Mar. 2008    (Pairings)

Code changes:

• Improved snp125 hgTrackUi and hgc displays. (Angie)
• Modified hgFind.c to use gbStatus.orgCat to distinguish native mRNAs from xeno when possible. (Angie)
• Extended axtSubsetOnT in axt.c to add axtGetSubsetOnT, similar to axtSubsetOnT except it modifies an axt instead of writing to a file, and has an option to not trim gaps adjacent to the range. Extended axtPrintTraditional to add axtPrintTraditionalExtra, with optional reversing of the printed coordinates (for when the axt alignment was created on sequence that was already reverse-complemented). (Angie)
• Added slNameListFromStringArray to inc/common. (Angie)
• Ongoing work on ENCODE submission pipeline. (Galt)
• Minor update to Ensembl gene automation script. (Hiram)
• Modified txCds/txInfoAssemble to handle CCDS. (Jim)
• Ongoing work on instinct. (Jing, Zack)
• Changed some functions in hgTracks/config.c to static to make code easier to read. (Mark)
• Added function sqlSignedForgiving in retroMrnaInfo.c -- converts string to signed integer; unlike atol assumes * all of string is number. (Robert)

Data changes:

• Added Affy Human Exon column to GeneSorter. (Andy)
• Reloaded snp128ExceptionDesc for hg18 and mm9. (Angie)
• Changed refGene's idXref setting to use its own name2 field in several organisms. (Angie)
• Added local definition and description of hg18 tajD and tajdSnp to emphasize that they were lifted from hg17. (Angie)
• Added search index for rnaGene. (Fan)
• Finished mm8 Ensembl gene update. (Hiram)
• Work on bosTau4 , choHof1 (sloth) browsers. (Hiram)
• Added ce4 nucleosome map density graphs. (Hiram)
• Added ponAbe2 nscan gene predictions. (Mark)
• Added retroMrnaInfo to hg18. (Robert)