sync to upstream
Implemented centered context mapping scheme. Merge-level implementation of centered context mapping on credit.
Fixed iterator in order to map left-most bases
Merged and added command line flags for centered and LR exact schemes w/ and w/o mapping on credit
Merge pull request #1 from yoheirosen/Centered

Merge work done on centered scheme and mapping on credit into master
fixed errors in offsets for centered scheme
Merge pull request #2 from yoheirosen/Centered

fixed errors in offsets for centered scheme
Fixed issues with centered offset and credit mapping; reverse matched LR exact credit mapping
Merge pull request #3 from yoheirosen/Centered

Fixed issues with centered offset and credit mapping; reverse matched LR...
Fixed templates so swig can wrap vector<pair<int64_t,size_t>>
Merge pull request #4 from yoheirosen/Centered

Fixed templates so swig can wrap vector<pair<int64_t,size_t>>
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