public static int?AnyIndelCoveredInMate(IEnumerable <IndelSite> readIndelPositions,
BamAlignment readWithoutIndels, BamAlignment readWithIndels, int anchorSize = 0)
{
if (readIndelPositions == null || !readIndelPositions.Any())
{
return(null);
}
if (readWithIndels.IsReverseStrand())
{
readIndelPositions = readIndelPositions.Reverse();
}
foreach (var indelPosition in readIndelPositions)
{
var coveredInR1 =
readWithoutIndels.ContainsPosition(indelPosition.PreviousMappedPosition - anchorSize, readWithIndels.RefID) &&
readWithoutIndels.ContainsPosition(indelPosition.NextMappedPosition + anchorSize, readWithIndels.RefID);
if (coveredInR1)
{
return(indelPosition.PreviousMappedPosition);
}
}
return(null);
}
private bool AnchoredRegionContainsUnanchoredEnds(BamAlignment read1, BamAlignment read2)
{
var read1UnanchoredStart = read1.Position - (read1.CigarData.GetPrefixClip());
var read1UnanchoredEnd = read1.GetLastBasePosition() + (read1.CigarData.GetSuffixClip());
return(read2.ContainsPosition(read1UnanchoredStart, read1.RefID) ||
read2.ContainsPosition(read1UnanchoredEnd, read1.RefID));
}