GeCo++

GeCo++: a C++ library for genomic features computation and annotation in the presence of variants

http://bioinformatics.oxfordjournals.org/content/27/9/1313.full

http://bioinformatics.emedea.it/geco/

http://bioinformatics.emedea.it/geco/doc/geco_tutorial.html, this tutorial give a comparison between GeCo and R on NGS analysis. So you could learn much about R/bioconductor.