Merge pull request #63 from fnothaft/pair-haplotype-argmax

Updated pair haplotype scoring method
Refactoring variant callers to take in partition set. Adds flank for calling variants with assembly.
Merge pull request #64 from fnothaft/add-flanks-to-gather

Add flanks to gather
Fixing kmer spur removal code, and adding tests for spur removal. Making spur removal active by default during assembly.
Adding heuristic to trim paths that are not covered by many reads. Also, adding larger data set for unit tests.
Adding heuristic to avoid entering loops.
Updated configuration files and debug logging for assembler.