/// <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);
}
}
public void InvalidateSAMWriteTextWriter()
{
SAMAlignmentHeader header = new SAMAlignmentHeader();
try
{
SAMFormatter.WriteHeader(null, header);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"SAM Formatter P2 : Successfully validated the exception");
}
}
/// <summary>
/// Writes the header to output stream
/// </summary>
/// <param name="header"></param>
private void WriteHeader(SAMAlignmentHeader header)
{
if (!Header && !HeaderOnly)
{
return;
}
if (UnCompressedBAM || BAMOutput)
{
// Incase of compressed bamoutput uncompressed file will be compressed before sending it to output stream.
bamformatter.WriteHeader(header, bamUncompressedOutStream);
}
else
{
SAMFormatter.WriteHeader(header, writer);
}
}
