/// <summary>
/// Reads ambiguously placed due to genomic reads.
/// This step requires mate pair information to resolve the ambiguity about placements of repeated sequences.
/// </summary>
/// <param name="deltaAlignmentCollection">Alignment between reference genome and reads.</param>
/// <returns>List of DeltaAlignments after resolving repeating reads.</returns>
private static IEnumerable <DeltaAlignment> RepeatResolution(DeltaAlignmentCollection deltaAlignmentCollection)
{
return(RepeatResolver.ResolveAmbiguity(deltaAlignmentCollection));
}
/// <summary>
/// Reads ambiguously placed due to genomic reads.
/// This step requires mate pair information to resolve the ambiguity about placements of repeated sequences.
/// </summary>
/// <param name="alignmentBetweenReferenceAndReads">Alignment between reference genome and reads.</param>
/// <returns>List of DeltaAlignments after resolving repeating reads.</returns>
private List <DeltaAlignment> RepeatResolution(IList <IEnumerable <DeltaAlignment> > alignmentBetweenReferenceAndReads)
{
return(RepeatResolver.ResolveAmbiguity(alignmentBetweenReferenceAndReads));
}