v159-final - 15 May 2007    (Pairings)

Code changes:

• Made survey link configurable from hg.conf. (Andy)
• Fixed baseColorOverdrawQInsert in hgTracks/cds.c to correctly handle ++ and +- strand alignments. (Angie)
• Fixed bug in convertCoordUsingPsl in hgTracks/cds.c that caused a block to be incorrectly colored yellow when tStart < 3; fixed by changing tStart from unsigned to int. (Angie)
• Added hSetDb to cartCopyCustomTracks in lib/cart.c to prevent customFactory parsing from setting it as a side effect of hGetMinIndexLength. (Angie)
• Changed the knownGeneAcc termRegex in trackDb.ra to be pickier so it doesn't trigger on symbols like TP53; also, made it handle the new UCSC Genes IDs with or without the dot-version suffix. (Angie)
• Added semiShortCircuit refGeneAcc search so knownGeneAcc won't eclipse NM_s. (Angie)
• Fixed 64-bit bug in gsidTable.c. (Fan)
• Bug fixes & mods to gsidMember.c (Galt)
• Cleaned up the hprintf escape in gsidTable.c. (Galt)
• Made automatic use of vgProbes and vgAllProbes in knownToVisiGene.c now that mm8 has frog as well as native alignments. (Galt)
• Added SELFMAP command to migrate vgProbes psls to vgAllProbes. (Galt)
• Fixed parasol bug in use of sizeof on array parameter. (Galt)
• Mods to hapMap SNPS UI & monomorphism filter in hgTrackUI.c. (Heather)
• Mods to hapMapTrack.c. (Heather)
• Mods to hgc.c for hapMap ortho alleles. (Heather)
• Mod to hgTables to allow BED graph tracks to output all or selected fields. (Hiram)
• Fixed reordering checkbox on config page to automatically update page. (Hiram)
• Fixed up MIME parsing in cheapcgi.c to eliminate bad IE behavior of full path names with spaces being passed where not expected. (Hiram)
• Modified hgGene.c to make refSeq accession appear by summary when summary is available. (Jim)
• Added support for CT database to DNA coloring feature in hgc.c. (Kate)
• Added function to lib/hash.c to get number of entries in a hash. (Mark)
• Added options to include unaligned in stats in pslStats. (Mark)
• Added LOWELAB #ifdefs to hgTracks.c, hgc.c. (Todd, Patricia)

Data changes:

• Removed index on chromEnd in several .sql files. (Angie)
• Work on felCat3 multiz run. (Heather)
• Mods to several .ra files to make refSeq accession appear by summary when summary is available. (Jim)
• Fixed kg1ToKg2/kg2ToKg3 renaming issue. (Jim)
• Began prep for ENCODE hg17 to hg18 migration, loaded TBA alignments. (Kate)
• More work on hg18 28-way phastCons. (Kate)