v143-final - 26 Sep. 2006

Code changes:

• Fix for default option for microarray combine option when nothing is set in the cart. added to hgTrackUi.c (Andy)
• Added expRatioDrawItemsWithExons() to expRatioTracks.c. Moving some microarrays to new method in expRatioTracks.c, hgTracks.c, and hgc.c (Andy)
• Added lfsFromBedAndGrouping() in expRatioTracks.c as the default microarray track filter for tracks using new microarrayGroups.ra scheme. (Andy)
• Added doExpRatio() to expClick.c to average array data defined by microarrayGroups.ra file. hgc.c and hgc.h both use this (Andy)
• New functions added to microarry.c and microarray.h to use microarray lib functions that average array data defined by microarrayGroups.ra file (Andy)
• Release of new CGI, hgCgiData (Andy)
• Moved session loading code from hgSession.c to hui.c. Added new functions to hgSession.c for log in, link/email function to create bookmarkable/shareable URL for loading session into hgTracks and instructions for creating links. Plus UI improvements (Angie)
• hgTracks can now share session loading code in hui.c. Added Session link to hgTracks hotlinks. Session loading code removed from hgTracks.c so now called in cartNew in cart.c. Other functions added to cart.c for session loading: cartLoadUserSession() and cartLoadSettings() (Angie)
• Moved html print functions to the htmlPrintHelperLibrary from hgGene.c, hgGenome.c, hgSubj.c, hgTables.c, hgTracks.c, lowLabTracks.c, hgc.c (Daryl)
• Added snp125Extended loading and sorting of snp125 track based on color in variation.c and added snp125Extended to snp125.c (Daryl)
• Added functions for InterPro tracks for HIV database browser in hgTracks.c and added track to hgc.c. Added disease class codes for Genetic Association Database (GAD) track in hgTracks.c (Fan)
• VisiGene and qaPushQ fixes and update of build scripts (Galt)
• Changes to list comparisons for gv tables in hgc.c and added new type for src link in gvUi.c (Belinda)
• Code for new SNP Array track and other changes for SNPs in hgc.c. snpReadSeq.c utility to read dbSNP SNP FASTA files. Created autosql files for new SNP Array track (Heather)
• Added hTvDropDownClassVisOnly() function for limiting visibility of a track to a single visibility to hui.c and used it in hgTracks.c, config.c and hgTrackUi.c (Hiram)
• Bug fixes and release of hgCustom. cgiTableFieldWithMsg() and cgiMakeTextAreaDisaleable() in cheapCgi.c adds a text are that allows grayout out. (Kate)
• Fix in hgTracks.c for PDF output page. Program for fake homozygosity data. (Jim)
• Bug fix in ccdsInfo.c and ccdsMkTables.c for multiple versions of the same RefSeq accession appearing in ccdsInfo table. Added new MGC status code mgcStatusTbl.c and mgcImport.c. Other fixes to hgGenenericMicroarray.c and its makefile. (MarkD)

Data changes:

• Moved some microarrays over to new method (Andy)
• Added Genetic Association Database track (new release) for hg17 (Fan)
• Added InterPro Domains track (for HIV database) (Fan)
• New exact search for wgRna so items can be found by name even if they also appear in gene descriptions (Rachel)
• Added Affy10K and 100K to snpArray composite track. Split Affy500K into two components (Heather)
• Added semiShortCircuit for SNP searches (Heather)