Initial checkin on localAlignment branch
Implemented crude local alignment

It still needs testing!
Use local match function
Temp checkin

This code still needs to be debugged.
Fixed boundaryChunk issue with local alignment
Incremental checkin
Incremental checkin
Incremental checkin
Incremental checkin
Incremental checkin
Added LocalScorer and GlobalScorer

Added scorers for annotating each aligned chunk with a score.
The score is broken into components for sizing score, contig score,
optical score.
Incremental Checkin
Added SeqCoord and MapCoord
Incremental Checkin
Incremental Checkin
Incremental Checkin
Incremental checkin
Incremental checkin
Incremental Checkin
Incremental Checkin