v169-final - 16 Oct. 2007    (Pairings)

Code changes:

• Removed some hgGenome and trackDbCustom code that was a duplicate of existing code in hdb.c. (Andy)
• Use new printLiftOverGenomeList in hgLiftOver, which doesn't require the databases to exist. Changed several routines to disregard whether a database exists. (Angie)
• Extended doJaxQTL in hgc.c to handle the cross-species-mapped bed4 case. (Angie)
• Several mods to browser build automation scripts. (Angie)
• Added utils/mergeOverlapBed4.pl to merge overlapping bed4 items with the same name and sort by chrom, chromStart, a name-descending. (Angie)
• Added support for bedRegionIn/bedRegionOut option for 2bit files. (Daryl)
• Ongoing work on Instinct. (Fan)
• Ongoing work on ENCODE pipeline. (Galt)
• Added function to lib/common.c to create an slPair from a string. (Galt)
• Added checks to hgTrackDb to check for subGorup data between subtrack and composite parent. (Galt)
• Added handler for a few signals that will log errors (lib/cart.c, lib/cheapcgi.c. (Galt)
• Added new trackDb setting: scoreFilterMax. (Hiram)
• Added special case in hgc.c/printCustomUrl() for targetScanS. (Hiram)
• Ongoing work on hgHeatmap. (Jing, Zack)
• Added super-track support to DNA extended case/color feature. (Kate)

Data changes:

• Mapped mm8 MGI QTLs to hg18. (Angie)
• Reran mergeOverlapBed4.pl on hg18 jaxQTL* and reloaded. (Angie)
• Added ce5 WS180 -- masked sequence only, no DB, plus ce4/ce5 liftOver chains. Needed for modENCODE. (Angie)
• Added a FlyBase transcript IF column to dm GeneSorter. (Angie)
• Added strPur2 human proteins track. (Brian)
• Updated hg18 targetScanS track data. (Hiram)
• More work on mm9 30-way alignment, exoniphy, Alt Events. (Hiram)
• Generated hg18/marmoset alignments for Elliott. (Kate)
• Added contrastGene .as file. (Mark)