public static List <BamAlignment> GetSupplementaryAlignments(this BamAlignment alignment, Dictionary <string, int> refIdMapping = null)
{
var supplementaries = new List <BamAlignment>();
if (!alignment.HasSupplementaryAlignment())
{
return(supplementaries);
}
var tag = alignment.GetStringTag("SA");
var supplementaryAlignments = tag.Split(new[] { ';' }, StringSplitOptions.RemoveEmptyEntries);
foreach (var supplementaryAlignment in supplementaryAlignments)
{
// SA tag format: (rname,pos,strand,CIGAR,mapQ,NM ;)+
var splitTag = supplementaryAlignment.Split(new[] { ',' }, StringSplitOptions.RemoveEmptyEntries);
var tagChromosome = splitTag[0];
var tagPosition = int.Parse(splitTag[1]);
var tagStrand = splitTag[2];
var tagCigar = splitTag[3];
var tagMapq = splitTag[4];
var tagNM = splitTag[5];
var bamAlignment = new BamAlignment()
{
Position = tagPosition - 1, // Deal with the fact that BamAlignment obj is 0-indexed, whereas SA is 1-indexed
CigarData = new CigarAlignment(tagCigar),
};
if (tagStrand == "-")
{
bamAlignment.SetIsReverseStrand(true);
}
if (refIdMapping != null)
{
Console.WriteLine(tagChromosome);
bamAlignment.RefID = refIdMapping[tagChromosome];
}
supplementaries.Add(bamAlignment);
}
return(supplementaries);
}
// TODO maybe this should be extension of CigarAlignment?
public static bool CigarMatchesPattern(this BamAlignment alignment, string pattern)
{
if (alignment.CigarData.Count != pattern.Length)
{
return(false);
}
for (int i = 0; i < pattern.Length; i++)
{
var op = alignment.CigarData[i];
if (pattern[i] != op.Type)
{
return(false);
}
}
return(true);
}
/// <summary>
/// Copy constructor.
/// </summary>
public BamAlignment(BamAlignment a)
{
AlignmentFlag = a.AlignmentFlag;
Bases = a.Bases;
Bin = a.Bin;
CigarData = new CigarAlignment(a.CigarData.ToString());
FragmentLength = a.FragmentLength;
MapQuality = a.MapQuality;
MatePosition = a.MatePosition;
MateRefID = a.MateRefID;
Name = a.Name;
Position = a.Position;
Qualities = new byte[a.Qualities.Length];
Array.Copy(a.Qualities, Qualities, Qualities.Length);
RefID = a.RefID;
TagData = a.TagData;
_endPosition = a._endPosition;
}
/// <summary>
/// Returns the "one-based end position", which is the end position of the alignment + 1 (Isas BamAlignment is zero-based). Note that this will return a different value (-1) than before the update to Isas BamAlignment.
/// </summary>
/// <param name="alignment"></param>
/// <returns></returns>
public static int OneBasedEndPosition(this BamAlignment alignment)
{
// NOTE this will return a different value (-1) than before the update to Isas BamAlignment. Nothing internal to Pisces is using it.
return(alignment.GetEndPosition() + 1);
}
/// <summary>
/// Returns the "one-based position" of the alignment (Isas BamAlignment is zero-based).
/// </summary>
/// <param name="alignment"></param>
/// <returns></returns>
public static int OneBasedPosition(this BamAlignment alignment)
{
return(alignment.Position + 1);
}
public static string StringRepresentation(this BamAlignment alignment)
{
return(string.Format("{0},{1},{2},{3},{4}", alignment.Name, alignment.RefID, alignment.Position,
alignment.FragmentLength, alignment.CigarData, alignment.MateRefID, alignment.MatePosition));
}
//TODO may be able to get rid of this and just use !IsPrimary
public static bool IsSecondary(this BamAlignment alignment)
{
return((alignment.AlignmentFlag & 256) != 0);
}
/// <summary>
/// Return the position of the last base in the read. Note that this is equivalent to the result before the update to Isas BamAlignment at c348f98 in PICS-847.
/// </summary>
/// <param name="alignment"></param>
/// <returns></returns>
public static int GetLastBasePosition(this BamAlignment alignment)
{
return(alignment.GetEndPosition());
}
public static bool ContainsPosition(this BamAlignment alignment, long position, int refId, bool startInclusive = true, bool endInclusive = true)
{
return(alignment.RefID == refId &&
(startInclusive ? alignment.Position <= position : alignment.Position < position) &&
(endInclusive ? alignment.GetLastBasePosition() >= position : alignment.GetLastBasePosition() > position));
}
public static int OneBasedEndPosition(this BamAlignment alignment)
{
return(alignment.GetEndPosition() + 1);
}
