/// <summary>
/// Writes specified sequence alignment to stream.
/// The output is formatted according to the BAM structure.
/// </summary>
/// <param name="sequenceAlignmentMap">SequenceAlignmentMap object.</param>
/// <param name="writer">Stream to write.</param>
/// <param name="createSortedFile">If this flag is true output file will be sorted.</param>
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();
}
/// <summary>
/// Writes BAM header to the specified stream in BAM format.
/// </summary>
/// <param name="header">SAMAlignmentHeader object</param>
/// <param name="writer">Stream to write.</param>
public void WriteHeader(SAMAlignmentHeader header, Stream writer)
{
if (header == null)
{
throw new ArgumentNullException("header");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string samHeader;
if (_refSequences == null)
{
_refSequences = SortSequenceRanges(header.GetReferenceSequenceRanges());
}
using (StringWriter strwriter = new StringWriter(CultureInfo.InvariantCulture))
{
SAMFormatter.WriteHeader(header, strwriter);
samHeader = strwriter.ToString();
}
int samHeaderLen = samHeader.Length;
byte[] bytes = System.Text.ASCIIEncoding.ASCII.GetBytes(samHeader);
byte[] bamMagicNumber = new byte[4] {
66, 65, 77, 1
};
// write BAM magic number
writer.Write(bamMagicNumber, 0, 4);
// Length of the header text
writer.Write(Helper.GetLittleEndianByteArray(samHeaderLen), 0, 4);
//Plain header text in SAM
writer.Write(bytes, 0, bytes.Length);
// number of reference sequences
writer.Write(Helper.GetLittleEndianByteArray(_refSequences.Count), 0, 4);
for (int i = 0; i < _refSequences.Count; i++)
{
int len = _refSequences[i].ID.Length;
byte[] array = System.Text.ASCIIEncoding.ASCII.GetBytes(_refSequences[i].ID);
writer.Write(Helper.GetLittleEndianByteArray(len + 1), 0, 4);
writer.Write(array, 0, len);
writer.WriteByte((byte)'\0');
writer.Write(Helper.GetLittleEndianByteArray((int)_refSequences[i].End), 0, 4);
}
}
/// <summary>
/// Writes BAM header to the specified stream in BAM format.
/// </summary>
/// <param name="header">SAMAlignmentHeader object</param>
/// <param name="writer">Stream to write.</param>
public void WriteHeader(SAMAlignmentHeader header, Stream writer)
{
if (header == null)
{
throw new ArgumentNullException("header");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string samHeader;
if (this.refSequences == null)
{
this.refSequences = header.GetReferenceSequenceRanges();
}
using (StringWriter strwriter = new StringWriter(CultureInfo.InvariantCulture))
{
SAMFormatter.WriteHeader(strwriter, header);
samHeader = strwriter.ToString();
}
int samHeaderLen = samHeader.Length;
byte[] bytes = Encoding.UTF8.GetBytes(samHeader);
byte[] bamMagicNumber = { 66, 65, 77, 1 };
// write BAM magic number
writer.Write(bamMagicNumber, 0, 4);
// Length of the header text
writer.Write(Helper.GetLittleEndianByteArray(samHeaderLen), 0, 4);
//Plain header text in SAM
writer.Write(bytes, 0, bytes.Length);
// number of reference sequences
writer.Write(Helper.GetLittleEndianByteArray(this.refSequences.Count), 0, 4);
foreach (SequenceRange range in this.refSequences)
{
int len = range.ID.Length;
byte[] array = Encoding.UTF8.GetBytes(range.ID);
writer.Write(Helper.GetLittleEndianByteArray(len + 1), 0, 4);
writer.Write(array, 0, len);
writer.WriteByte((byte)'\0');
writer.Write(Helper.GetLittleEndianByteArray((int)range.End), 0, 4);
}
}
/// <summary>
/// Writes SAMAlignedSequence to specified stream.
/// </summary>
/// <param name="header">Header from SAM object.</param>
/// <param name="alignedSeq">SAMAlignedSequence object.</param>
/// <param name="writer">Stream to write.</param>
public void WriteAlignedSequence(SAMAlignmentHeader header, SAMAlignedSequence alignedSeq, Stream writer)
{
if (header == null)
{
throw new ArgumentNullException("header");
}
if (alignedSeq == null)
{
throw new ArgumentNullException("alignedSeq");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
_refSequences = SortSequenceRanges(header.GetReferenceSequenceRanges());
WriteAlignedSequence(alignedSeq, writer);
}