//public static string GetZezValue(this SAMAlignedSequence sam)
//{
// return GetOptionValue(sam, "ZE", "Z");
//}
public static void WriteFastq(this SAMAlignedSequence sam, StreamWriter sw, bool posAsPaired = false)
{
if (posAsPaired)
{
sw.WriteLine(string.Format("@{0} {1}", sam.QName, sam.Pos));
}
else
{
sw.WriteLine("@" + sam.QName);
}
sw.WriteLine(sam.GetQuerySequenceString());
sw.WriteLine("+");
sw.WriteLine(sam.GetQualityScoresString());
}
public string SAMToString(SAMAlignedSequence sam)
{
if (sam == null)
{
return null;
}
return string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}",
sam.QName,
(int)sam.Flag,
sam.RName,
sam.Pos,
sam.MapQ,
sam.CIGAR,
sam.MRNM,
sam.MPos,
sam.ISize,
sam.GetQuerySequenceString(),
sam.GetQualityScoresString(),
(from of in sam.OptionalFields
select string.Format("{0}:{1}:{2}", of.Tag, of.VType, of.Value)).Merge("\t"));
}
public static void WriteFasta(this SAMAlignedSequence sam, StreamWriter sw)
{
sw.WriteLine(">" + sam.QName);
sw.WriteLine(sam.GetQuerySequenceString());
}