v158-preview - 24 Apr. 2007    (Pairings)

Code changes:

• Added support for Switchgear TSS. (Andy)
• Modified hgGene/otherOrgs.c to improve efficiency when diging up orthologs. (Angie)
• Rescued/updated liftRMAlign.pl for automation scripts. (Angie)
• Fixed hgFindSpecCustom -- added a flag (reEntered) when hgFindSpecFromRa recurses on include files to prevent hgFindSpecPolish from being called multiple times on the included records, causing too many backslash-escapes. (Angie)
• Appended date to sequence file name to reduce problems w/pushes. (Angie)
• More work on history/atom*. (Brian)
• Ongoing work on GSID. (Fan)
• Changed pbGlobal.c logic to searh kgXref table instead of knownGene for mrnaID for KGIII. (Fan)
• Added way to detect protein-PSL custom tracks even if PSL header is missing (customFactory.c). (Galt)
• Added SV clones links to hgc.c. (Heather)
• Fixed a missing x3 bug in blat protein/DNA alignments. (Jim)
• Modified hgTrackUi.c to include update time for data in track table. (Kate)
• Changed gff.c to trim spaces from GFF gene names. (Mark)
• Added track handler for encodeGencodeGeneMar07 track. (Rachel)

Data changes:

• Added Switchgear TSS track to hg17 & hg18. (Andy)
• Added geneTable setting for quering position for genomeUrl links for several organisms in hgGene/hgGeneData. (Angie)
• Ongoing work on ornAna1. (Angie)
• Generated gasAcu1 self chains (special request). (Angie)
• Added ce4 human proteins track. (Brian)
• Changed knowToTreeFam to knownToTreefam. (Fan)
• Fixed missing Jax levels 5, 6 for 13000 pictures in VisiGene. (Galt)
• Added cnpLocke SV data. (Heather)
• Work on several worms. (Hiram)
• Comparative alignments between oryLat1 and tetNig1, danRer4. (Hiram)
• Fixed PB link problem in hgGeneData/Mouse. (Jim)
• Added Gencode RACEfrags track. (Rachel)