void makePair(Alignment& a, Alignment& b, Alignment& x, Alignment& y)
{
initMate(a, x);
initMate(b, y);
Feature spacer;
getSpacer(a, b, spacer);
int insert = a.Length + spacer.getLength() + b.Length;
// Add in mate pair info
x.MateRefID = b.RefID;
x.matePosition(b.position());
x.InsertSize = insert;
y.MateRefID = a.RefID;
y.matePosition(a.position());
y.InsertSize = -1 * insert;
// Update Mapping information appropriately
x.SetIsReverseStrand(a.IsReverseStrand());
x.SetIsMateReverseStrand(b.IsReverseStrand());
y.SetIsReverseStrand(b.IsReverseStrand());
y.SetIsMateReverseStrand(a.IsReverseStrand());
}
bool isValidPair(Alignment& a, Alignment& b)
{
Feature spacer;
getSpacer(a, b, spacer);
int gap = spacer.getLength();
// Calculate the correct size of the insert
// REMEMBER: negative gaps mean our values overlap
// pair must be oriented correctly
// (5'--------->3' 3'<---------5')
return gap >= MIN_GAP && gap <= MAX_GAP
&& !a.IsReverseStrand() && b.IsReverseStrand();
}
