/*
* TRTR: Trim Reads of Tandem Repeats
*
* This tool removes tandem repeats from ends of unaligned sequencing
* reads (leaving one copy). This prevents reads that don't span the
* repeated region from overlapping and leading to innaccurate SNPs
* calls.
* 
* The maximimum repeat length is adjustable (use 1 to trim only
* homopolymers).
*
* The "aggressive" option should not be touched in general. Setting to
* 0 will prevent the program from trimming to exactly 1 copy of the
* repeat, instead leaving between 1 and 2 copies. Why this would be
* useful, I don't know.
* 
* This program could also be a useful first step before assembly. More
* testing needs to be done.
*
* Future updates will add the capability for trimming reads in aligned
* BAM files.
*/