// Attempt to resolve a predicted overlap between s1 and s2
// Returns true if there overlap was found and the overhang of s2 is placed in outString
bool ScaffoldRecord::overlapResolve(const ResolveParams& params, const std::string& s1, const std::string& s2,
const ScaffoldLink& link, std::string& outString) const
{
// Attempt to find an overlap between these sequences
int expectedOverlap = -1 * link.distance;
// If the maximum overlap was not set, set it to the expected overlap * 3 stddev
int upperBound = 0;
if(params.maxOverlap == -1)
upperBound = static_cast<int>(expectedOverlap + 3.0f * link.stdDev);
else
upperBound = params.maxOverlap;
// Calculate the best match
Match match;
bool overlapFound = OverlapTools::boundedOverlapDP(s1, s2, params.minOverlap, upperBound, params.maxErrorRate, match);
if(overlapFound)
{
SeqCoord overlapCoord = match.coord[1];
SeqCoord overhangCoord = overlapCoord.complement();
outString = overhangCoord.getSubstring(s2);
return true;
}
else
{
return false;
}
}
// Attempt to resolve a predicted overlap between s1 and s2
// Returns true if there overlap was found and the overhang of s2 is placed in outString
bool ScaffoldRecord::overlapResolve(const ResolveParams& params, const std::string& s1, const std::string& s2,
const ScaffoldLink& link, std::string& outString) const
{
// Attempt to find an overlap between these sequences
int expectedOverlap = -1 * link.distance;
#ifdef DEBUGRESOLVE
std::cout << "Attempting overlap resolve of link to " << link.endpointID << " expected distance: " << link.distance << " orientation: " << link.edgeData.getComp() << "\n";
#endif
// If the maximum overlap was not set, set it to the expected overlap * 3 stddev
int upperBound = 0;
if(params.maxOverlap == -1)
upperBound = static_cast<int>(expectedOverlap + 3.0f * link.stdDev);
else
upperBound = params.maxOverlap;
// Calculate the best match
Match match;
bool overlapFound = OverlapTools::boundedOverlapDP(s1, s2, params.minOverlap, upperBound, params.maxErrorRate, match);
if(overlapFound)
{
#ifdef DEBUGRESOLVE
std::cout << "Overlap found, length: " << match.coord[1].length() << "\n";
#endif
SeqCoord overlapCoord = match.coord[1];
SeqCoord overhangCoord = overlapCoord.complement();
outString = overhangCoord.getSubstring(s2);
return true;
}
else
{
return false;
}
}
