// parses sequence.
private void ParseSequences(SequenceAlignmentMap seqAlignment, BioTextReader bioReader, bool isReadOnly)
{
while (bioReader.HasLines && !bioReader.Line.StartsWith(@"@", StringComparison.OrdinalIgnoreCase))
{
string[] tokens = bioReader.Line.Split(tabDelim, StringSplitOptions.RemoveEmptyEntries);
SAMAlignedSequence alignedSeq = new SAMAlignedSequence();
alignedSeq.QName = tokens[0];
alignedSeq.Flag = SAMAlignedSequenceHeader.GetFlag(tokens[1]);
alignedSeq.RName = tokens[2];
alignedSeq.Pos = int.Parse(tokens[3], CultureInfo.InvariantCulture);
alignedSeq.MapQ = int.Parse(tokens[4], CultureInfo.InvariantCulture);
alignedSeq.CIGAR = tokens[5];
alignedSeq.MRNM = tokens[6].Equals("=") ? alignedSeq.RName : tokens[6];
alignedSeq.MPos = int.Parse(tokens[7], CultureInfo.InvariantCulture);
alignedSeq.ISize = int.Parse(tokens[8], CultureInfo.InvariantCulture);
string message = alignedSeq.IsValidHeader();
if (!string.IsNullOrEmpty(message))
{
throw new FormatException(message);
}
ISequence refSeq = null;
if (RefSequences != null && RefSequences.Count > 0)
{
refSeq = RefSequences.FirstOrDefault(R => string.Compare(R.ID, alignedSeq.RName, StringComparison.OrdinalIgnoreCase) == 0);
}
ParseQualityNSequence(alignedSeq, Alphabet, Encoding, tokens[9], tokens[10], refSeq, isReadOnly);
SAMOptionalField optField = null;
for (int i = 11; i < tokens.Length; i++)
{
optField = new SAMOptionalField();
string optionalFieldRegExpn = OptionalFieldLinePattern;
if (!Helper.IsValidRegexValue(optionalFieldRegExpn, tokens[i]))
{
message = string.Format(CultureInfo.CurrentCulture, Resource.InvalidOptionalField, tokens[i]);
throw new FormatException(message);
}
string[] opttokens = tokens[i].Split(colonDelim, StringSplitOptions.RemoveEmptyEntries);
optField.Tag = opttokens[0];
optField.VType = opttokens[1];
optField.Value = opttokens[2];
message = optField.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new FormatException(message);
}
alignedSeq.OptionalFields.Add(optField);
}
seqAlignment.QuerySequences.Add(alignedSeq);
bioReader.GoToNextLine();
}
}
