void SMRTSequence::MakeSubreadAsMasked(SMRTSequence &subread,
DNALength subreadStart, int subreadEnd) {
//
// This creates the entire subread, but masks out the portions
// that do not correspond to this insert.
//
SetSubreadBoundaries(subread, subreadStart, subreadEnd);
subread.Copy(*this);
DNALength pos;
for (pos = 0; pos < subreadStart; pos++) { subread.seq[pos] = 'N'; }
for (pos = subreadEnd; pos < length; pos++) { subread.seq[pos] = 'N'; }
// This is newly allocated memory, free it on exit.
subread.deleteOnExit = true;
}
