v157-final - 17 Apr. 2007    (Pairings)

Code changes:

• Mods and bug fixes to enable SwitchDB TSS track. (Andy)
• Major mods to cgapSageFind. (Andy)
• Added SNP info to CGAP SAGE track. (Andy)
• Added findSnpClusters utility to find SNP clusters interfering with SAGE analysis. (Andy)
• Added enhancements to hgTables to support search on gene symbols. (Angie)
• Modified sqlRandomSampleWithSeed to perform the uniquifying and randomizing on a limited-size temporary table to avoid thrashing on mega-row tables. (Angie)
• Modified hgc -- when making a View Table Schema link, if parentWigMaf has been passed in directly by CGI, use that as the track name for hgTables. (Angie)
• Fixed hgTables/schema.c to prevent segv for wigMaf tracks-in-progress that don't yet specify wiggle table. (Angie)
• Added Treefam links to hgGene details page. (Fan)
• Added "Select Subjects" to GSID top bar, enhanced logic in checking if subject selection is needed. (Fan)
• Added some asserts, changed some sprintf()s to safef()s. (Fan)
• More work on VisiGene postcript output code. (Galt)
• Moved color-by-strand for ENCODE Stanford NRSF track. (Heather)
• Fine-tuned HapMap SNPs display. (Heather)
• Created/updated docs for medaka. (Hiram)
• Added bedOrBlocks -- creates a BED that is the union of all blocks of a list of beds. (Jim)
• Modified display of bacEndPairs in full mode (no connecting line). (Jim)
• Updated UCSC Genes make doc to use $db and $tempDb rather than hg18. (Jim)
• Fiddled with blank lines in hgTracksUi, hgTracks, etc. (Jim)
• Separated model info from methods section in hgGenes. (Jim)
• Fixed GTF bug where frame was incorrectly converting from GFF/GTF files, fixed off-by-one error in setting frame from GTF. (Mark)
• Removed end index and key length restrictions on genePreds. (Mark)
• Added new code to add quality data to MAFs. (Rico)

Data changes:

• Added new setting idXref to refGene in several assemblies to support pasitng/uploading identifier aliases in hgTables. (Angie)
• Created knownToTreefam table to add Treefam links to hgGene. (Fan)
• Added ENCODE Stanford NRSF track. (Heather)
• Added default position instructions that were lost from hgcentraltest dbDb for several assemblies. (Hiram)
• Created fr1 to fr2 liftOver. (Hiram)
• Added caeRem2/cb3 chains and nets. (Hiram)
• Generated several cb3 tracks. (Hiram)
• Reworked oryLat1 annotated multiz5way MAFs. (Hiram)
• Changed ordering of worms chain/nets on hgTracks page to reflect phulogeny. (Hiram)
• Updated BAC End Pairs and Fosmids displays to make connecting arrowheads darker. (Jim)
• Fixed Mammal Cons, added phastCons for 28way in hg18 trackDb.ra. (Kate)
• Loaded N-SCAN track for equCab1. (Mark)
• Added oryLat1 xeno RefSeqs. (Mark)
• Added public orfeome track (orfeomeMrna). (Mark)
• Updated several ENCODE tracks: Gencode Genes track, added UVA DNA Replication missing data, added new subtracks for H9, IMR90 and K562 cells to the Duke/NHGRI DNase track and removed 2 subtracks created by older methods. (Rachel)