Fixes to HMM to add reference padding.
Change locuspredicate to unique read mapped predicate
Merge pull request #61 from fnothaft/hmm-padding

Fixes to HMM to add reference padding.
Merge pull request #62 from hammerlab/update-predicate

Change locuspredicate to unique read mapped predicate
Adding hidden model and argmax algorithm for scoring haplotype pairs.
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.
Merge pull request #70 from fnothaft/update-config-and-debug

Update config and debug