Add option to remove alignment gaps '~' in the filtered consensus sequence; fixes bug #67 where deletions are replaced with 'N' but not removed so truncated alleles are not interpreted properly
Fix bug #69 by increasing the sensitivity of long-read (consensus sequence) alignment, decreasing the mismatch penalty to 1 from default 3
Change '~' to '-' and rename parameter from -v to -r
Merge pull request #68 from ckennedy-nmdp/bug67

Add option to remove alignment gaps '~' in the filtered consensus sequen...