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Changed the package name from PileOMeth to MethylDackel. It is unfortunate that the temporary "PileOMeth" name stuck around for so long.
Fixed the plotting where the sometimes the plotted lines escape the bounds of the graph. The cause for this was that read #2 was being ignored when the graph bounds were being computed.
Added the --requireFlags/-r option, which is equivalent to the -f option in samtools. The default is 0, which requires nothing.