v154-final - 13 Mar. 2007    (Pairings)

Code changes:

• Increased memory usage limit in bedIntersect, as suggested by Mike Pheasant. (Angie)
• Tweaked mrna->all_mrna in findSelectedTrack (hgTables) to match what is done in getFullTrackList. (Angie)
• Mods to agpToLift: recognize -revStrand when passed in, add strand column to output instead of modifying sequence names. (Angie)
• Fix to hgTables when there is an intersection, all fields selected, and Galaxy output. (Belinda)
• Fix to chainToPsl.c to get right bases to calculate score. (Brian)
• Moved location of VG search results tempfile to trash/vg (VisiGene.c). (Galt)
• Replaced hgGenome/upload.c code w/CT library calls. (Galt)
• Ongoing work on hg17 HapMap SNPs. (Heather)
• Added user-defined regions support in TB. (Hiram)
• Replaced top-level trash names w/subdirs in several files, replaced customTrackTrashFile with trashDirFile in several places, allowed use of Kate's defines for prefix names in trashDir files. (Hiram)
• Ongoing work on KG III. (Jim)
• Added optional syntenic net step to automation/doBlastzChainNet.pl. (Kate)
• Added timestamp to stepper msg in automation/HgStepManager.pm. (Kate)
• Added -oppositeStrand option to overlapSelect. (Mark)
• Added support for non-protein-coding mRNAs to GenBank processing. (Mark)
• Several mods to Ensembl gene support. (Robert)

Data changes:

• Reloaded gasAcu1 Ensembl genes using latest BioMart interface. (Angie)
• Added ornAna1/galGal3 blastz, chains, nets. (Angie)
• Added equCab2 blastz, human proteins. (Fan)
• Updates to protein DB. (Fan)
• Fixed key length limit on allenBrainUrl primary key. (Galt)
• Added several shrew 2X x-alignments. (Kate)
• More work on hg18 25-way multiple alignment. (Kate)
• Generated alignments between galGal3 and fr1/fr2. (Hiram)
• Added felCat3 N-SCAN. (Mark)
• Added Eponine TSS prediction track to hg17. (Rachel)