/// <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)); }