v179-final - 1 Apr. 2008 (Pairings)

Code changes:

Added yellow/blue color options to hgTracks (mailing list request), removed large amount of obsolete track-specific code. (Andy)
Added tests for zero-length range (bitCount of 0) to bitSetRange, bitCountRange and bitClearRange in lib/bits.c. Previously, when startIx was a multiple of 8, endByte was 1 less than startByte and 16 bits were set. (Angie)
Added hConnectLogicalDb() and trackDbConn() to inc/hdb.c to support loading trackDb from DB other than the regular DB. (Fan)
Added logic in hgTracks/expRatioTracks.c to connect to a logical DB to support VM server systems. (Fan)
Ongoing work on ENCODE DCC submission pipeline. (Galt)
Final work on Ensembl genes automation doEnsGeneUpdate script. (Hiram)
Fixed an edge condition in bedCompatibleExtension in lib/bed.c. (Jim)
Modified lib/txCommon.c accession-checking routine to handle CCDS accessions. (Jim)
Modified txBedToGraph so that vertices from CCDS edges are not snapped in a way that would cause the transcript to be made smaller. (Jim)
Ongoing work on instinct. (Jing, Zack)
Fixed GenBank bugs associated with a forced reload. (Mark)