v221-preview - 9 December 2009    (Pairings)

Code changes:

• Interleave accesses from two open udcFile handles to the same part of a URL/file. (Angie)
• Add root option to tdbQuery. (Brian)
• Add support for SAM and BAM files to ENCODE validator. (Brian)
• Updates to ENCODE submission pipeline. (Galt, Kate)
• Fixed neg-strand issue for PCR psl output. (Galt)
• Catch (big*, bam) loader when it tries to open a missing file. (Galt)
• TrackDb clean-up. (Hiram, Jim)
• Turned c/n into chainNet composite for all cows. (Hiram)
• tdbQuery - trackDb query tool. (Jim)
• trackDbPatch - tool to surgically add to .ra files. (Jim)
• Several trackDb "rewriter" tools. (Jim)
• Right-click menu for Imagev2. (Larry)
• Fixed bug in matrix (plus/minus buttons were failing when no matrix exists). (Tim)
• Tied the chrom image drag-jump feature to advanced Javascript features. (Tim)
• Work on flat tracks for subtrack drag-reorder. (Tim)

Data changes:

• More ENCODE data. (Brian, Tim)
• galGal3 quality track. (Angie)
• Added Gene Network link for hg19 hgGene page. (Fan)
• Added two more subtracks for Illumina SNP arrays. (Fan)
• Added Retroposed Genes to hg19. (Rachel)
• phastCons and phyloP for 46-way for hg19. (Hiram)
• Adding ctgPos2 track for oryCun2. (Hiram)
• Added some Fire Lab experiments to ce6. (Hiram)
• California Condor alignments for galGal3. (Mark)