/// <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>
/// Create a sequence enumerator that filters the reads and adds them to the depth of coverage counter
/// if necessary.
/// </summary>
/// <param name="bamFileName">Filename to load data from</param>
/// <returns>Enumerable set of ISequence elements</returns>
public static IEnumerable <CompactSAMSequence> GetNuclearAndMitochondrialReads(string bamFileName)
{
var parser = new BAMSequenceParser(bamFileName);
var header = parser.GetFileHeader();
foreach (var chr in Regions.Split('\n'))
{
var chr2 = chr.Trim();
var split = chr2.Split('\t');
var locs = split.Skip(1).Select(x => Convert.ToInt32(x)).ToList();
var name = split[0];
if (!header.ReferenceSequences.Any(z => z.Name == name))
{
name = "chr" + name;
if (!header.ReferenceSequences.Any(z => z.Name == name))
{
continue;
}
}
foreach (var v in parser.ParseRangeAsEnumerableSequences(bamFileName, name, locs[0], locs[1]))
{
yield return(v);
}
}
}
