// 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();
}
}
/// <summary>
/// Parse a single sequencer.
/// </summary>
/// <param name="bioText">sequence alignment text.</param>
/// <param name="alphabet">Alphabet of the sequences.</param>
/// <param name="referenceSequences">Reference sequences.</param>
private static SAMAlignedSequence ParseSequence(string bioText, IAlphabet alphabet, IList <ISequence> referenceSequences)
{
const int optionalTokenStartingIndex = 11;
string[] tokens = bioText.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);
ISequence refSeq = null;
if (referenceSequences != null && referenceSequences.Count > 0)
{
refSeq = referenceSequences.FirstOrDefault(R => string.Compare(R.ID, alignedSeq.RName, StringComparison.OrdinalIgnoreCase) == 0);
}
ParseQualityNSequence(alignedSeq, alphabet, tokens[9], tokens[10], refSeq);
SAMOptionalField optField = null;
string message;
for (int i = optionalTokenStartingIndex; i < tokens.Length; i++)
{
optField = new SAMOptionalField();
if (!Helper.IsValidRegexValue(OptionalFieldRegex, tokens[i]))
{
message = string.Format(CultureInfo.CurrentCulture, Properties.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];
alignedSeq.OptionalFields.Add(optField);
}
return(alignedSeq);
}
/// <summary>
/// Parse a single sequencer.
/// </summary>
/// <param name="bioText">sequence alignment text.</param>
/// <param name="alphabet">Alphabet of the sequences.</param>
public static SAMAlignedSequence ParseSequence(string bioText, IAlphabet alphabet)
{
const int optionalTokenStartingIndex = 11;
string[] tokens = bioText.Split(TabDelim, StringSplitOptions.RemoveEmptyEntries);
SAMAlignedSequence alignedSeq = new SAMAlignedSequence
{
QName = tokens[0],
Flag = SAMAlignedSequenceHeader.GetFlag(tokens[1]),
RName = tokens[2],
Pos = int.Parse(tokens[3]),
MapQ = int.Parse(tokens[4]),
CIGAR = tokens[5]
};
alignedSeq.MRNM = tokens[6].Equals("=") ? alignedSeq.RName : tokens[6];
alignedSeq.MPos = int.Parse(tokens[7]);
alignedSeq.ISize = int.Parse(tokens[8]);
ParseQualityNSequence(alignedSeq, alphabet, tokens[9], tokens[10]);
for (int i = optionalTokenStartingIndex; i < tokens.Length; i++)
{
SAMOptionalField optField = new SAMOptionalField();
if (!Helper.IsValidRegexValue(OptionalFieldRegex, tokens[i]))
{
throw new FormatException(string.Format(Properties.Resource.InvalidOptionalField, tokens[i]));
}
string[] opttokens = tokens[i].Split(ColonDelim, StringSplitOptions.RemoveEmptyEntries);
optField.Tag = opttokens[0];
optField.VType = opttokens[1];
optField.Value = opttokens[2];
alignedSeq.OptionalFields.Add(optField);
}
return(alignedSeq);
}