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

        private void WriteUncompressed(SequenceAlignmentMap sequenceAlignmentMap, Stream writer, bool createSortedFile)
        {
            SAMAlignmentHeader header = sequenceAlignmentMap.Header;
            if (createSortedFile && SortType == BAMSortByFields.ChromosomeNameAndCoordinates)
            {
                header = GetHeaderWithSortedSQFields(header, true);
                this.refSequences = header.GetReferenceSequenceRanges();
            }

            if (this.refSequences == null)
            {
                this.refSequences = header.GetReferenceSequenceRanges();
            }

            WriteHeader(header, writer);
            writer.Flush();
            if (createSortedFile)
            {
                WriteUncompressedSortedBAM(sequenceAlignmentMap, writer);
            }
            else
            {
                foreach (SAMAlignedSequence seq in sequenceAlignmentMap.QuerySequences)
                {
                    SAMAlignedSequence alignedSeq = seq;
                    this.ValidateSQHeader(alignedSeq.RName);
                    this.WriteAlignedSequence(alignedSeq, writer);
                    writer.Flush();
                }
            }

            writer.Flush();
        }