Disabling test of mysql database interface, as it's broken and we
probably don't need to support mysql
abstracted details of adding options to allow jobTree to use either argparse or optparse
formatting
fix for argparse based option parsing
typo in help message
fix isinstance check of OptionParser to detect OptionContainer instead.  This way OptionGroups and OptionParsers are supported and progressiveCactus doesnt get broken.
dont redive mysql vars if specified.  allows progressive cactus wrapper to override
Added extra variant of sorting function
add function to remove leaf from nxtree
Merge branch 'development' of git://github.com/benedictpaten/sonLib into development
divide bulkGets into maxBulkSetNumRecords chunks like we do for bulkSets
Fix to string join to fix overflow
Merge branch 'refs/heads/development' of git@github.com:benedictpaten/sonLib.git into HEAD
change max kt record size from 175M to 50M.  this is to address weird problems in bulk set from secondary db when doing full human mouse alignment.
Fixing overflow error in string join, another one
Merge branch 'refs/heads/development' of git@github.com:benedictpaten/sonLib.git into HEAD
Modifying compression function to deal with buffer overruns
Adding logging to compression routine for large sequences to be
compressed.
Changing fasta header decompose methods
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