/// <summary>
/// Parses the BAM file and returns the Header.
/// </summary>
private SAMAlignmentHeader GetHeader()
{
var header = new SAMAlignmentHeader();
RefSeqNames = new RegexValidatedStringList(SAMAlignedSequenceHeader.RNameRegxExprPattern);
_refSeqLengths = new List <int>();
ReadStream.Seek(0, SeekOrigin.Begin);
_deCompressedStream = null;
var array = new byte[8];
ReadUnCompressedData(array, 0, 8);
var lText = Helper.GetInt32(array, 4);
var samHeaderData = new byte[lText];
if (lText != 0)
{
ReadUnCompressedData(samHeaderData, 0, lText);
}
ReadUnCompressedData(array, 0, 4);
var noofRefSeqs = Helper.GetInt32(array, 0);
for (var i = 0; i < noofRefSeqs; i++)
{
ReadUnCompressedData(array, 0, 4);
var len = Helper.GetInt32(array, 0);
var refName = new byte[len];
ReadUnCompressedData(refName, 0, len);
ReadUnCompressedData(array, 0, 4);
var refLen = Helper.GetInt32(array, 0);
RefSeqNames.Add(Encoding.ASCII.GetString(refName, 0, refName.Length - 1));
_refSeqLengths.Add(refLen);
}
if (samHeaderData.Length != 0)
{
var str = Encoding.ASCII.GetString(samHeaderData);
using (var reader = new StringReader(str))
{
header = SAMParser.ParseSAMHeader(reader);
}
}
header.ReferenceSequences.Clear();
for (var i = 0; i < RefSeqNames.Count; i++)
{
var refname = RefSeqNames[i];
var length = _refSeqLengths[i];
header.ReferenceSequences.Add(new ReferenceSequenceInfo(refname, length));
}
return(header);
}
/// <summary>
/// The default constructor which chooses the default encoding based on the alphabet.
/// </summary>
protected AbstractBAMParser(string bamFileName)
{
BAMFileName = bamFileName;
RefSeqNames = new RegexValidatedStringList(SAMAlignedSequenceHeader.RNameRegxExprPattern);
_refSeqLengths = new List <int>();
ReadStream = new FileStream(bamFileName, FileMode.Open, FileAccess.Read, FileShare.Read);
ValidateReader();
Header = GetHeader();
RefSeqChunks = null;
LastChunk = null;
Filter = new BAMAccept();
}
