/// <summary>
/// Returns list of reference sequences present in this header.
/// </summary>
public IList <string> GetReferenceSequences()
{
List <string> refSequences = new List <string>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
refSequences.Add(tag.Value);
}
}
return(refSequences);
}
/// <summary>
/// Returns list of reference sequences name and length present in SQ header.
/// </summary>
public IList <ReferenceSequenceInfo> GetReferenceSequencesInfoFromSQHeader()
{
List <ReferenceSequenceInfo> refSequencesInfo = new List <ReferenceSequenceInfo>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
string refName = tag.Value;
long length;
tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "LN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null && long.TryParse(tag.Value, out length))
{
refSequencesInfo.Add(new ReferenceSequenceInfo(refName, length));
}
}
}
return(refSequencesInfo);
}
/// <summary>
/// Returns list of SequenceRanges objects which represents reference sequences present in this header.
/// </summary>
public IList <SequenceRange> GetReferenceSequenceRanges()
{
List <SequenceRange> ranges = new List <SequenceRange>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
string refName = tag.Value;
long length;
tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "LN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null && long.TryParse(tag.Value, out length))
{
SequenceRange range = new SequenceRange(refName, 0, length);
ranges.Add(range);
}
}
}
return(ranges);
}
