v136-final

Code changes:

• work on hgAutomate & hgRemoteScript (Angie)
• hgc.c mods for genomicSuperDups & IGTC (Angie)
• fixed compiler warnings (Angie, Hiram)
• new functions in expData.c to load rows of SQL table into a list & return it (Andy)
• work on phyloGif (Galt)
• changed vgGetText to a utility; build automatically only for hgwbeta branch (Galt)
• changed visiSearch to tolerate missing vgGetText files (Galt)
• mods to Human Mutation track display; changed table names (Belinda)
• mods to support snp126, variant BAC names (Heather)
• changed -noRandom to recognize non-canonical chrUn/NA/U (Gill)
• work on hgCustom (Kate)
• fixed problem w/tree image display on Conservation track desc. page (Kate)
• fixed blat problem w/sea urchin protein DNA alignments (from mailing list) (Jim)
• work on hgGenome (Jim)
• factored out code from various modules (esp. cytoBand) for reuse in hgGenome (Jim)
• work on chromGraph (Jim)
• mods to use trash sub-directories (Hiram)
• minor strand comparison bug fix in hgGene/mrnaDescriptions.c (Hiram)

Data changes:

• fixed strand for genomicSuperDups (Angie)
• added probe sequence FASTA for IGTC Gene Trap (Angie)
• added missing rn4 bigZips/upstream*.fa.gz files (Angie)
• added speciesCodonDefault line in Conservation block for several species (Ann)
• more work on Boreoeutherian browser (Brian)
• added rn4, hg18 & mm8 Superfamily tracks (Fan)
• built rn4 Proteome Browser (Fan)
• rebuilt rn4 kgProtMap (Fan)
• updated hg17 RGD QTL track (Fan)
• renamed hgMut tables to genomeVar (Belinda)
• added danRer4/rn4 chains/nets (Rachel)
• work on hg16 CNPs (Heather)
• mods to hg17 snp125 (Heather)
• work on hg17 snp126 (Heather)
• updated ENCODE MSA elements to fix off-by-one error (Kate)
• mods to ENCODE MSA data display (Kate)
• added ensGene, ensGtp data to mm8 & monDom4 (Hiram)