message: avoid hanging in super low entropy sequence
  We should never be running the entropy calculation past the read end. It won't
  ever support a haplotype call to do so.
  This change may very slightly change behavior of the algorithm in low entropy
  sequence regions.
diff: @@ -1266,19 +1266,16 @@ Allele AlleleParser::makeAllele(RegisteredAlignment& ra,
  // a dangerous game
  int start = pos - currentSequenceStart;
  double minEntropy = parameters.minRepeatEntropy;
  - // check first that' wer'e actually ina repeat... TODO
  - //cerr << "entropy of " << entropy(currentSequence.substr(start, repeatRightBoundary - pos)) << " is too low, " << endl;
  while (minEntropy > 0 && // ignore if turned off
  - repeatRightBoundary - currentSequenceStart < currentSequence.size() && //guard
  + // don't run off the end of the current sequence
  + repeatRightBoundary - currentSequenceStart < currentSequence.size() &&
  + // there is no point in going past the alignment end
  + // because we won't make a haplotype call unless we have a covering observation from a read
  + repeatRightBoundary < alignment.ENDPOSITION &&
  entropy(currentSequence.substr(start, repeatRightBoundary - pos)) < minEntropy) {
  - //cerr << "entropy of " << entropy(currentSequence.substr(start, repeatRightBoundary - pos)) << " is too low, ";
  - //cerr << "increasing rought boundary to ";
  ++repeatRightBoundary;
  - //cerr << repeatRightBoundary << endl;
  }
  - // now we
  - //cachedRepeatCounts[pos] = repeatCounts(pos - currentSequenceStart, currentSequence, 12);
  // edge case, the indel is an insertion and matches the reference to the right
  // this means there is a repeat structure in the read, but not the ref
  if (currentSequence.substr(pos - currentSequenceStart, length) == readSequence) {
  