/// <summary>
/// Parses a list of sparse sequences from the reader, one per contiguous
/// chromosome present in the reader. There is one SequenceItem per SnpItem with
/// either of the two alleles in the SnpItem (determined by the ParseAlleleOne property)
/// and at the same position in the sequence as the SnpItem.Position.
/// </summary>
/// <returns>Returns a list of sparse sequences containing Snp items that were read
/// from the reader, one sequence per contiguous chromosome number and
/// retaining the same position in the sequence as the chromosome position.</returns>
public IEnumerable <ISequence> Parse()
{
if (this.Filename == null)
{
throw new FieldAccessException("Filename");
}
if (this.Alphabet == null)
{
this.Alphabet = AmbiguousDnaAlphabet.Instance;
}
using (StreamReader txtReader = new StreamReader(this.Filename))
{
ISnpReader snpReader = new XsvSnpReader(txtReader, new[] { '\t' }, true, true, 0, 1, 2, 3);
snpReader.MoveNext();
List <ISequence> sequenceList = new List <ISequence>();
while (snpReader.Current != null)
{
sequenceList.Add(ParseOne(snpReader));
}
return(sequenceList);
}
}
public void XsvBvtSnpReaderSkipToChromosomePosition()
{
// Gets the expected sequence from the Xml
string filePath = _utilityObj._xmlUtil.GetTextValue(Constants.SimpleSnpNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"XsvSnpReader BVT: File Exists in the Path '{0}'.",
filePath));
using (StreamReader strReaderObj = new StreamReader(filePath))
{
XsvSnpReader rdr = new XsvSnpReader(
strReaderObj, new Char[1] {
'\t'
},
false, true, 0, 1, 2, 3);
// Validate with IsChromosomeSorted and IsChromosomePositionStarted set to false
rdr.MoveNext();
Assert.IsFalse(rdr.SkipToChromosomePosition(0));
// Validates the Comment Line Property
Assert.IsNull(rdr.CommentLine);
rdr.Dispose();
using (StreamReader strRdrObj = new StreamReader(filePath))
{
rdr = new XsvSnpReader(strRdrObj, new Char[1] {
'\t'
},
false, true, 0, 1, 2, 3);
rdr.MoveNext();
rdr.IsChromosomeSorted = true;
// Validate with IsChromosomeSorted property set
Assert.IsFalse(rdr.SkipToChromosomePosition(0, 0));
rdr.MoveNext();
rdr.IsChromosomePositionSorted = true;
// Validate with IsChromosomePositionSorted property set
Assert.IsFalse(rdr.SkipToChromosomePosition(0, 0));
// Logs information to the log file
ApplicationLog.WriteLine(
"XsvSnpReader BVT: Successfully validated the SkipToChromosomePosition() method");
Console.WriteLine(
"XsvSnpReader BVT: Successfully validated the SkipToChromosomePosition() method");
}
}
}
/// <summary>
/// Parses a list of sparse sequences from the reader, one per contiguous
/// chromosome present in the reader. There is one SequenceItem per SnpItem with
/// either of the two alleles in the SnpItem (determined by the ParseAlleleOne property)
/// and at the same position in the sequence as the SnpItem.Position.
/// </summary>
/// <param name="stream">Stream to be parsed.</param>
/// <returns>Returns a list of sparse sequences containing Snp items that were read
/// from the reader, one sequence per contiguous chromosome number and
/// retaining the same position in the sequence as the chromosome position.</returns>
public IEnumerable <ISequence> Parse(Stream stream)
{
if (this.Alphabet == null)
{
this.Alphabet = AmbiguousDnaAlphabet.Instance;
}
using (var reader = new StreamReader(stream))
{
ISnpReader snpReader = new XsvSnpReader(reader, new[] { '\t' }, true, true, 0, 1, 2, 3);
snpReader.MoveNext();
while (snpReader.Current != null)
{
yield return(ParseOne(snpReader));
}
}
}