private bool ReadsDoNotOverlap(BamAlignment read1, BamAlignment read2)
{
var overlaps = read1.OverlapsAlignment(read2);
if (overlaps)
{
return(false);
}
if (_treatHalfAnchoredAsUnanchored)
{
return(true);
}
// Check for S/M overlap, if half-anchoring is allowed
var read1ContainsUnanchoredRead2 = AnchoredRegionContainsUnanchoredEnds(read1, read2);
var read2ContainsUnanchoredRead1 = AnchoredRegionContainsUnanchoredEnds(read2, read1);
return(!(read1ContainsUnanchoredRead2 || read2ContainsUnanchoredRead1));
}
