This is a prototype of STRait Razor 4.0! Use at your own risk!
Seriously, I'm still developing this, but the general idea is
to apply alignment to STRs. While this make some people nervous
the idea is to apply it in such a way that that read alignment is
invariant to the STR motif found in that individual. The advantage
of this is that now we can decorate the haplotype identified
with genomic information.
The current implementation is written in C++ and integrated with R
using the Rcpp package.