v152-preview - 5 Feb. 2007    (Pairings)

Code changes:

• Include referenced objects/tables in stored autoSql for each table, so that we store complete definitions (so the autoSql parser doesn't die in hgTables). (angie).
• hgGenome configuration and help docs (ann, jim)
• Bug fix in hgSpeciesRna if filter not specified (robert).
• hgc - add length to protein comment (robert)
• pslCdnaGenomeMatch - bug fix to pass-through option (robert).
• chainOneTwo/pslOneTwo - fixc missing option specs (robert)
• hgNotYet.c for pages under construction(fan).
• gsidMember - add email addresses for contact info (galt)
• Fixed order dependency for members.o (galt)
• Choice and color mods to phenotype aassociation track (belinda)
• cvs-reports - tcl version change (rachel, mark)
• Ongoing hapmap development (heather)
• Complete human-mouse Window Masking (hiram)
• Documenting build process - $MACHTYPE (hiram)
• Custom Tracks - protection again corrupted trash files (kate)
• Custom Tracks - GTF format fix and documentation (kate)
• New version and docs for blat (jim)
• KG III development (jim)
• altSplice - improve debugging and replace hRangeQuery call with hChromQuery (jim)
• orthoSplice - ifdeff out some unused code (jim)
• Improve hash size in case altSplice used for contigs (jim)
• sequenceForBed - added -keepName option (jim)
• exonWalk - added -singleExonOk option (jim)
• addCluster - fix minus strand problem (jim)
• clusterPsl - add local clustering and memory leak fix (jim)
• altGraphX - fix canPack option ans .as file mod for tableDescriptions.pl (jim)
• Modify and document swissProt construction (jim)
• psl - add pslCmpTargetAndStrand (jim)
• Add rangeTrees for tracking non-overlapping intervals (jim)
• genoFind - bug fix for when db is empty (jim)
• doTableStatus - hgTables method for getting table status (bob)
• QA script - removed dependency on qateam in checkTrackUiLinks.csh by making wgetTableField.csh (bob)
• QA script - added support for encode and composite tracks to findLevel.csh (bob)
• QA script - added totalling to getTablesize.csh (bob)
• Fixed bug where ESTs' intron lines sometimes not drawn in dense mode (mark)

Data changes:

• Human Proteins track for bosTau2 (brian)
• Locus Variants track data reload (belinda)
• Fish comparatives - fugu, medaka, stickleback, tetraodon (hiram)
• felCat3 geneid track (hiram)
• Added augustus predictions for mouse, cat, chimp (mario)