char U2AssemblyReadIterator::nextLetter() {
assert(hasNext());
skip();
SAFE_POINT(offsetInCigar < cigar.size(), "CIGAR out of range", 0);
if(offsetInToken != cigar.at(offsetInCigar).count) { //staying in the current token
offsetInToken++;
} else { //current token is finished
advanceToNextToken();
offsetInToken = 1;
}
bool del = isDeletion();
char c = del ? '-' : read.at(offsetInRead); //TODO: hardcoded '-'
offsetInRead += !del; //adjust offsetInRead only when going through match token
return c;
}
String TextDiff::Change::appliedTo (const String& text) const noexcept
{
return text.substring (0, start) + (isDeletion() ? text.substring (start + length)
: (insertedText + text.substring (start)));
}
void U2AssemblyReadIterator::skip() {
while(hasNext() && !isMatch() && !isDeletion()) {
skipInsertion();
skipPaddingAndHardClip();
}
}