/// <summary>
/// Seek to the unaligned (and mate-unaligned) reads at the tail of the input file, and write them all out to the output file.
/// </summary>
private void WriteUnalignedReads(BamWriter writer)
{
Logger.WriteToLog("Writing unaligned reads");
using (var reader = new BamReader(_inputFile))
{
reader.JumpToUnaligned();
var read = new BamAlignment();
while (true)
{
var result = reader.GetNextAlignment(ref read, false);
if (!result)
{
break;
}
if (read.RefID != -1)
{
continue; // skip over last reads
}
writer.WriteAlignment(read);
}
}
}
