Now calculates maximum context length separately from working FMDPosition to allow extension-mapping in centered scheme
Made maxContext update correctly on extension of contexts.
Changed bound of left-right credit mapping search to ensure you don't go off-contig
Fixed bug where centered context restarts were failing due to apparent lack of context
Fixed issue with 0- vs 1-based offset of merged positions when mapping on credit
Orientation of credit merged positions
Corrected orientation in left-only credit merging
Fixed orientation in centered pinching. Typecast positions for credit merge to avoid off-contig merging
Corrected merge orientation on centered credit merging; safeguards to prevent off-contig merging
Merge pull request #5 from yoheirosen/Centered

Merge of Centered fork -- Implemented centered mapping with credit; bug fixes