Bio.IO.BAM.BAMFormatter.ValidateAlignment C# (CSharp) Method

        private SequenceAlignmentMap ValidateAlignment(ISequenceAlignment sequenceAlignment)
        {
            SequenceAlignmentMap seqAlignmentMap = sequenceAlignment as SequenceAlignmentMap;
            if (seqAlignmentMap != null)
            {
                ValidateAlignmentHeader(seqAlignmentMap.Header);
                if (CreateSortedBAMFile && SortType == BAMSortByFields.ChromosomeNameAndCoordinates)
                {
                    this.refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
                }
                else
                {
                    this.refSequences = seqAlignmentMap.Header.GetReferenceSequenceRanges();
                }

                return seqAlignmentMap;
            }

            SAMAlignmentHeader header = sequenceAlignment.Metadata[Helper.SAMAlignmentHeaderKey] as SAMAlignmentHeader;
            if (header == null)
            {
                throw new ArgumentException(Properties.Resource.SAMAlignmentHeaderNotFound);
            }

            ValidateAlignmentHeader(header);

            seqAlignmentMap = new SequenceAlignmentMap(header);
            if (CreateSortedBAMFile && SortType == BAMSortByFields.ChromosomeNameAndCoordinates)
            {
                this.refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
            }
            else
            {
                this.refSequences = seqAlignmentMap.Header.GetReferenceSequenceRanges();
            }

            foreach (IAlignedSequence alignedSeq in sequenceAlignment.AlignedSequences)
            {
                SAMAlignedSequenceHeader alignedHeader = alignedSeq.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
                if (alignedHeader == null)
                {
                    throw new ArgumentException(Properties.Resource.SAMAlignedSequenceHeaderNotFound);
                }

                SAMAlignedSequence samAlignedSeq = new SAMAlignedSequence(alignedHeader);
                samAlignedSeq.QuerySequence = alignedSeq.Sequences[0];
                seqAlignmentMap.QuerySequences.Add(samAlignedSeq);
            }

            return seqAlignmentMap;
        }