* Partially reorganized things by creating a header file. This will facilitate possible library creation.
* Added preliminary BED support. Note that unlike samtools, if at least 6 columns are given then this will honour the strand designator. Orientation is not strictly used for this, but rather strand of origin (e.g., specifying '+' will only include reads originating from the top strand). Either using a 3-column BED file or placing a "." in column 6 will include reads originating from any strand.
* Added preliminary support for non-directional libraries, at least if the XG auxiliary tag is included in alignments (as is done by Bison and bismark).
* The getStrand() function was changed such that getStrand() & region.strand can be used to determine overlaps.