string FastaReference::getTargetSubSequence(FastaRegion& target) {
if (target.startPos == -1) {
return getSequence(target.startSeq);
} else {
return getSubSequence(target.startSeq, target.startPos - 1, target.length());
}
}
/**
* Say if a subsequence is invalid (if it has a pipe or a $ is invalid)
* @return true if invalid
*/
bool SubSequence::isInvalid() const
{
int end = startPos_ + size_ ;
if (end > motherSequence_->getSize())
{
return true;
}
int * subSeq = getSubSequence();
for(int i = 0; i<size_; i++)
{
int current = subSeq[i];
if ((current == 1) || (current == 2))
{
return true;
}
}
return false;
}