/// <summary>
/// Create a sequence enumerator that filters the reads and adds them to the depth of coverage counter
/// if necessary.
/// </summary>
/// <param name="fileName">Filename to load data from</param>
/// <returns>Enumerable set of ISequence elements</returns>
private IEnumerable <CompactSAMSequence> createSequenceProducer(string fileName, DepthOfCoverageGraphMaker coveragePlotter = null, bool alsoGetNuclearHits = false)
{
if (!Skip_DepthOfCoveragePlot && !Helper.IsBAM(fileName))
{
Skip_DepthOfCoveragePlot = true;
Output.WriteLine(OutputLevel.Error, "Warning: No coverage plots can be made without an input BAM File");
}
IEnumerable <CompactSAMSequence> sequences;
if (!alsoGetNuclearHits)
{
var parser = new BAMSequenceParser(Filename);
if (ChromosomeName != string.Empty)
{
parser.ChromosomeToGet = ChromosomeName;
sequences = parser.Parse();
}
else
{
sequences = parser.Parse();
}
}
else
{
sequences = BAMNuclearChromosomeReadGenerator.GetNuclearAndMitochondrialReads(fileName);
}
//Filter by quality
return(ReadFilter.FilterReads(sequences, coveragePlotter));
}
/// <summary>
/// Helper method to parse the given filename into a set
/// of ISequence elements.
/// </summary>
/// <param name="fileName">Filename to load data from</param>
/// <returns>Enumerable set of ISequence elements</returns>
internal IEnumerable <ISequence> ParseFile(string fileName)
{
ISequenceParser parser = SequenceParsers.FindParserByFileName(fileName);
if (parser == null)
{
parser = new FastAParser(fileName);
}
//else if (parser is Bio.IO.FastQ.FastQZippedParser)
//{
// Console.WriteLine("Filtering FastQ File");
// var filter = new Bio.Filters.FastQZippedQualityTrimmedParser(fileName);
// return ReadFilter.FilterReads(filter.Parse());
//}
if (parser is Bio.IO.BAM.BAMSequenceParser && ChromosomeName != string.Empty)
{
var b = parser as Bio.IO.BAM.BAMSequenceParser;
b.ChromosomeToGet = ChromosomeName;
}
return(ReadFilter.FilterReads(parser.Parse()));
}
