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...
redhat lacks pidof.  safer/easier to just not delete boilerplate header
Merge pull request #74 from janders3-nmdp/dont_kill_headerfile

redhat lacks pidof.  safer/easier to just not delete boilerplate header
misnamed variables.
Merge pull request #75 from janders3-nmdp/issue_53_ad_nauseum

misnamed variables.
fix issue 76 with the power of regex
Merge pull request #77 from janders3-nmdp/allow_fq_suffix

fix issue 76 with the power of regex