public static bool OverlapsAlignment(this BamAlignment read1, BamAlignment read2)
{
var r2StartIsInR1 = read1.ContainsPosition(read2.Position, read2.RefID);
var r2EndIsInR1 = read1.ContainsPosition(read2.GetLastBasePosition(), read2.RefID);
var r1StartIsInR2 = read2.ContainsPosition(read1.Position, read1.RefID);
var r1EndIsInR2 = read2.ContainsPosition(read1.GetLastBasePosition(), read1.RefID);
return((r2StartIsInR1 || r2EndIsInR1 || r1StartIsInR2 || r1EndIsInR2));
}
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));
}