v152-final - 12 Feb. 2007    (Pairings)

Code changes:

• hgSession polishing (angie)
• trfBig.c -- When input is stdin, make a more unique temp file name so multiple trfBig processes can run simultaneously on a host (necessary for cluster runs). (angie)
• simplePartition.pl -- Added logic to glom small sequences together into <$chunkSize groups, so that scaffold-based assemblies don't end up with one .lst per tiny sequence. (angie)
• pslCDnaGenomeMatch.c -- allow multiple top hits instead of only best hit (robert)
• GSID-specific top bar (fan)
• Made password more strict for GSID (galt)
• Reran BlastPs for otherORgs in Known Gene (galt)
• AllenBrain updates: checkImages, cleanImages (galt)
• SynBlastp bug fix: missing fields and missing index (galt)
• visiGeneLoad compiler warnings fixed (galt)
• Mods to build scripts (galt)
• Continuing devolopment of hapmap SNPs: filters, hapmapAllelesUi, combining population tables (heather)
• Moved blat and other temp files to use trashDirFile() (hiram)
• ggMrnaAli.h -- Add sourceType to the ggMrnaAli structure (hiram)
• tfbsConsSites.h -- Add TFBS_SITES_CUTOFF_MINIMUM define (hiram)
• rangeTree.h -- Add val to the range structure, and the function rangeTreeFindEnclosing() (hiram)
• Switched GO-term lookup to more stable protein accession instead of displayID (kate)
• Added doMetaData methods to hgTables (bob)
• agxToXml parser (jim)
• Ongoing KGIII work: altSplice, altGtraphX, exonWalk (jim)
• genomeGraph mods (jim)
• New programs: txEdgeBed, txEdgeOrtho, txGraph, txBedTotxg, txPslToBed, txgToAgx, txgTrim (jim)
• ggCluster, ggGraph enhancements (jim)
• hgLoadGenePred -- add option to disable validation for debugging (mark)
• chromAnn.c -- removed use on non-posix unlocked stdio functions (mark)
• overlapSelect.c -- added ability to cleanup selectTable memory to allow checking for memory leaks (mark)

Data changes:

• ornAna1 platypus rebuild to sync with NCBI (angie)
• wormbase track for hg18 (brian)
• Melanogaster proteins track for hg18 (brian)
• wgRna track for hg18 (fan)
• Adding tracks to horse browser (fan)
• Changed to links.ra format for IDbases (belinda)
• Fish comparatives -- medake, fugu, stickleback, tetraodon, zfish (hiram)
• Cat geneid track (hiram)