Save changes needed to submit to UCSC in Jun 2010.

Save changes needed to submit to UCSC in Jun 2010.

Some of those changes include:
  * modifying the list of variables to include in the ddf
  * making it easier to set the MapAlgorithm.
  * Return information about the condor scripts so I can make a
    condor dagman script to run all the compression jobs

Perhaps some parts of this should be moved into the main
htsworkflow. I can see wanting the code to batch convert
srf/qseqs to fastq being more generally useful.