/// <summary>
/// Make a PDF depth of coverage plot for the given file and MT DNA name.
/// Can be called after the reads are all processed.
/// </summary>
/// <param name="BAMFileName"></param>
/// <param name="outputFileName"></param>
/// <returns></returns>
public void OutputCoverageGraphAndCSV(string outputFilePrefix)
{
//Now to make the plot
var r = new RInterface();
List <RInterface.OptionalArgument> args = new List <RInterface.OptionalArgument>()
{
new RInterface.OptionalArgument("type", "l")
};
r.PlotPDF(Enumerable.Range(0, StaticResources.CRS_LENGTH).Select(x => (double)(x + 1)), depthCounts, outputFilePrefix + "Coverage.pdf", "Depth of Coverage", "mtDNA Position", "Depth", null, args);
StreamWriter sw = new StreamWriter(outputFilePrefix + "Coverage.csv");
sw.WriteLine("Pos,Depth");
for (int i = 0; i < depthCounts.Length; i++)
{
sw.WriteLine((i + 1).ToString() + "," + depthCounts[i].ToString());
}
sw.Close();
}
public MitoPaintedAssembler() : base()
{
#if !NO_R
rInt = new RInterface();
#endif
}