v177-preview - 26 Feb. 2008    (Pairings)

Code changes:

• Added utils/reTraceUtils/reTraceFixMaf/reTraceFixMaf.c -- a utility for resequencing trace work. (Andy)
• Added some missing calls to hLookupStringsInTdb in lib/hdb.c/hTrackDb. (Angie)
• Added automation subdir to scripts target to utils/makefile so make alpha will install. (Angie)
• Fixed gcc4.1 compiler warnings in altSplice dir. (Brian)
• Added support for loading old-style mafFrames format to inc/mafFrames.h/.c. (Brian)
• Added support for new mafFrames format to hgTracks/wigMafTrack.c. (Brian)
• Added better headers, all modes working in ratStuff/mafToProtein/mafToProtein.c. (Brian)
• Ongoing GSID work. (Fan)
• Fixed/updated hgGene/ctd.c. (Fan)
• Updated hgGE URL in hgGene/gad.c. (Fan)
• Added CTD section to hgGene/hgGene.h. (Fan)
• Ongoing work on Ensembl gene automation. (Hiram)
• Ongoing work on instinct. (Jing)
• Ongoing work on ENCODE submission pipeline. (Kate)
• Added clarification for minimum size of sequences to hgBlat.c. (Jim)
• Modified several files to have genePredCheck and hgLoadGenePred report errors on invalid chroms instead of aborting. (Mark)
• Added flag to several mafFrames files to indicate if frame is on an exon bound; fixed inconsistency in table columan and struct name in a backwards compatible manner. (Mark)
• Changed hgGene/altSplice.c to use hgvGfx. (Mark)
• Added reverse complement display mode in main browser window. (Mark)
• Removed old JK_WARN hack that was added to several makefiles when warnings were enabled only for some modules. (Mark)

Data changes:

• Added support for xrefLookup and xrefOrg settings to hgNearData/Mouse/mm9/columnDb.ra, to allow translation of names in columnDb.ra lookup queries. Added those settings to flyOrtholog specs for databases whose dmBlastTab table has CG* IDs instead of FlyBase's preferred FBgn* IDs. (Angie)
• Added hg18 MKAR tracks. (Belinda)
• Added hg18 CTD data. (Fan)
• Updated HuGE link and allenBrain links in hgGene/hgGeneData/Human/links.ra. (Fan)
• Added Dec07 freeze TBA alignments from Margulies lab to hg18, added work around for problem caused when viewing base level when frames are missing. (Kate)