Add clipping heuristic to indel realigner

[fnothaft]

Currently, the indel realigner code unclips all reads when locally realigning. This is OK (we won't wind up with worse alignments) but we may be missing out on the opportunity to realign some reads. I believe that we could have a clipping heuristic that would improve this—something like whether the base was previously clipped and has a low quality score.

[fnothaft]

Closing as won't fix. We will probably EOL the indel realigner post 1.0.0.