Added inexact matching in centered and credit cases
Fixed failure to actually mismatch map centered contexts
Temporary check for off-contig merging; need to find source of problem
Changed default mismatch flag to no mismatches
minor edit to properly display incorrect sentinel positions
Annotated some unannotated methods
fast and extension mapping-friendly mismatch extend implementation
Replaced overwritted mismatchmap method
Restart if condition on existence of mismatched extension fails for mismatch extend; mismatch restart works perfectly; all other context schemes work perfectly; credit implemented.
Merge pull request #6 from yoheirosen/Centered

Merging in Centered -- LR exact : note that inexact doesn't work yet with this--use inexact restart, slow with restarts but gives correct results