/// <summary>
/// Reads a FASTQ entry
/// Note that this assumes the ILMN format (4 lines per read). FASTQ files with multiline
/// sequences will likely cause issues
/// </summary>
/// <returns>Returns false if no more entries are available.</returns>
public bool GetNextFastqEntry(ref BoltRead read)
{
// grab the next entry
bool foundProblem = false; string header;
if ((header = reader.ReadLine()) == null) return false;
if ((read.Bases = reader.ReadLine()) == null) foundProblem = true;
if ((reader.ReadLine()) == null) foundProblem = true;
if ((read.Qualities = reader.ReadLine()) == null) foundProblem = true;
if (foundProblem)
{
throw new ApplicationException(
string.Format("ERROR: Unable to read the entire FASTQ entry in {0}. Is the file truncated?",
FileName));
}
read.Header = header;
if (! SkipAllReadNameParsing)
{
// parse the secondary information
Match headerMatch = headerRegex.Match(header);
if (! headerMatch.Success)
{
throw new ApplicationException(string.Format("Unexpected FastQ header {0}", header));
}
read.UnparsedName = headerMatch.Groups[1].Value;
if (headerMatch.Groups.Count > 2)
{
read.ReadNum = int.Parse(headerMatch.Groups[2].Value);
read.IsFiltered = (headerMatch.Groups[3].Value[0] == 'Y');
read.Index = headerMatch.Groups[4].Value;
}
// parse the read name
if (! SkipReadNameParsing)
{
if (headerMatch.Groups.Count != 5 || !read.ParseReadName())
{
throw new ApplicationException(string.Format("Invalid field count in FastQ header {0}", header));
}
}
}
return true;
}
/// <summary>
/// Writes the FASTQ entry
/// </summary>
public void WriteFastqEntry(BoltRead read)
{
// sanity check
if (!IsOpen)
{
throw new ApplicationException("ERROR: An attempt was made to write a FASTQ entry to an unopened file.");
}
if (read.Header != null)
{
_writer.WriteLine(read.Header);
}
else if (read.UMI != null)
{
_writer.WriteLine(string.Format("@{0}:{1}:{2}:{3}:{4}:{5}:{6}:{7} {8}:{9}:0:{10}",
read.InstrumentName,
read.RunID,
read.FlowcellID,
read.Lane,
read.Tile,
read.X,
read.Y,
read.UMI,
read.ReadNum,
(read.IsFiltered ? 'Y' : 'N'),
read.Index));
}
else
{
_writer.WriteLine(string.Format("@{0}:{1}:{2}:{3}:{4}:{5}:{6} {7}:{8}:0:{9}",
read.InstrumentName,
read.RunID,
read.FlowcellID,
read.Lane,
read.Tile,
read.X,
read.Y,
read.ReadNum,
(read.IsFiltered ? 'Y' : 'N'),
read.Index));
}
_writer.WriteLine(read.Bases);
_writer.WriteLine("+");
_writer.WriteLine(read.Qualities);
}
