- present list of datasets in selection control as description/dataset-name, e.g. "Hela cells/092713_MM1"
- modify y axis and xlimits to display the entire range of depth graph.
- y-axis now always intersects x-asis at y=0.
- change bowtie options to only keep those alignments that are unique within a statum.   This essentially make the filtering step to remove duplicate alignments and poor quality alignments unnecessary.   The dowside is that any attempt to align with zero mismatches results in an error.   Apparently the -m option of bowtie cannot take a zero argument.
- modify how statistics are calculated and exported.   There was an error in calculating of total alignment total.  Necesscitated a corresponding change to sql_enter_stats.
Lots and lots of changes to mds/qarp.
- mainly moved read-depth calculation into a incremental process in pure-R.  No more python code, no more preconstruction of read depth across a bunch of genes.
- now can specify a bunch of BAM files, a factor vector, a GTF file, and a gene name to get a pvalue for the profile across that gene.