v186-final - 8 July 2008    (Pairings)

Code changes:

• Added stderr log statement to lib/jksql.c when hConnectCentral fails over, diagnostic stderr messages to sqlTableOk in lib/jksql.c. (Angie)
• Added pid to cartTrace messages in lib/cart.c to allow matchup with pre-cart messages. (Angie)
• Added support for new orthologous allele table setting for snp12* (orangutan in addition to chimp and macaque). (Angie)
• Swapped dm3 chain/net for dp4. (Angie)
• Fixed problem in hgSession.c with js items appearing before http headers. (Angie)
• Mod to hgLoadBed.c -- when writing the tab file, if there is a write failure, exit immediately instead of loading part of the table. (Angie)
• More work on adding custom MAF tracks. (Brian)
• Mods to lib/hdb.c to get the db from the scientific name and the nib path from the dbDb table. (Brian)
• Mods to hgc.c -- add link to native DB for xenoRefGene item, handle getting DNA for a species without an active DB. (Brian)
• Mod to lib/web.c -- don't output hotlinks bar if DB isn't active. (Brian)
• Ongoing work on GSID. (Fan)
• Expanded max hash size limits in inc/hash.h. (Galt)
• Mods to lib/customFactory.c -- Fixed absolute reference to /trash/, added noComment optino to the hgLoadBed and hgLoadWiggle loaders. (Hiram)
• Added noHistory option for custom tracks. (Hiram)
• Fixed broken intersection in lib/wigDataStream.c when given BED file. (Hiram)
• Mod to hgTracks/wigTrack.c to take care of behavior where wigTotalHeight is called multiple times -- limitVisibility sets track height properly once the first time and we don't want wigTotalHeight to reset it. (Hiram)
• Mods to txCds/txCdsPick/txCdsPick.c to make transferExceptions work with CCDS. (Jim)
• More work on ENCODE DCC validator. (Larry)
• Added support for group defaultIsClosed. (Larry)
• Removed depreciated regexpfiltering from das.c, which was preventing modern cleints from correctly filtering by type. (Mark)
• Mod to lib/sqlProg.c -- report error on missing hg.cong entrries rather than generating a bogus command line. (Mark)
• Mod to makeDb/hgTrackDb/hgTrackDb.c -- added check for -raName being a simple file name. (Mark)
• Mods to more clearly makr and distinguish between parent/child and super/composite tracks. (Tim)
• Ongoing work on instinct and TCGA. (Zack, Steve0

Data changes:

• Added Positive Selection Genes track to hg18. (Adam, Brian)
• Added snp129 for hg18. (Angie)
• Initial work on taeGut1 (zebra finch) browser. (Brian)
• ORegAnno track updates for hg18, mm9, dm3, sacCer1. (Belinda)
• More work on laminB1Super track for hg18. (Mike)