public SAMAlignedSequence ReadSAMAlignedSequence()
{
if (_parser.IsEOF())
{
return(null);
}
return(_parser.GetAlignedSequence(true));
}
/// <summary>
/// Gets Aligned seqeunces in the Specified BAM file.
/// </summary>
/// <param name="textReader">BAM file stream.</param>
private IEnumerable <SAMAlignedSequence> GetAlignedSequence(Stream bamStream)
{
bool isFilterRequired = IsFilterApplied();
bool display = true;
while (!bamparser.IsEOF())
{
SAMAlignedSequence alignedSequence = bamparser.GetAlignedSequence(false);
if (isFilterRequired)
{
display = Filter(alignedSequence);
}
if (display)
{
yield return(alignedSequence);
}
}
}
// Search the BAM file for the next valid read aligned against the current contig.
// Update read/base pairs statistics.
private void Search_Reads(BAMParser parser, ref SAMAlignedSequence next_alignment, string contig_name,
ref long number_of_aligned_reads, ref long number_of_aligned_base_pairs, ref long number_of_used_reads,
ref long number_of_used_base_pairs, Queue <Padded_Read> read_queue, long current_position)
{
while (next_alignment != null &&
!next_alignment.IsDummyRead &&
next_alignment.RName == contig_name &&
(next_alignment.Pos - 1) == current_position)
{
// The next alignment overlaps with current position, so continue.
number_of_aligned_reads++;
number_of_aligned_base_pairs += next_alignment.QuerySequence.Count;
// Maybe we should let the mininum alignment quality be a parameter.
// We currently leave it for the user to pre-filter the BAM file.
if (next_alignment.MapQ > 0)
{
number_of_used_reads++;
number_of_used_base_pairs += next_alignment.QuerySequence.Count;
read_queue.Enqueue(new Padded_Read(next_alignment));
}
#region Parse BAM file until next alignment is found
if (!parser.IsEOF())
{
next_alignment = parser.GetAlignedSequence(true);
while ((next_alignment == null || next_alignment.RName == "*" || next_alignment.IsDummyRead) && !parser.IsEOF())
{
next_alignment = parser.GetAlignedSequence(true);
}
}
else
{
next_alignment = null;
}
#endregion Parse BAM file until next alignment is found
}
}
/// <summary>
/// Gets Aligned sequences in the Specified BAM file.
/// </summary>
/// <param name="bamStream"></param>
private IEnumerable <SAMAlignedSequence> GetAlignedSequence(Stream bamStream)
{
bool isFilterRequired = IsFilterApplied();
bool display = true;
while (!bamparser.IsEOF())
{
SAMAlignedSequence alignedSequence = bamparser.GetAlignedSequence(false);
//TODO: The parser should probably never return a null sequence
//this may be a band aid over a lurking problem, fix in future
if (alignedSequence != null)
{
if (isFilterRequired)
{
display = Filter(alignedSequence);
}
if (display)
{
yield return(alignedSequence);
}
}
}
}
