Added a multi-mapping percent filter
Added a multi-mapping percent filter

    - If secondary RNA alignments are allowed, there will be
      many false positive calls where nearly 100% of the reads
      supporting the alternative allele are from secondary RNA
      alignments (not primary alignments).  Added a filter now
      for calls where 90% or more of the reads supporting the
      alternative allele come from secondary mappings.  In other
      words, at least 10% of the reads need to be the primary
      mapping.  This filter is mostly relevant for RNA variants.

    - Renamed variable names to be consistent with rest of code

    - Renamed filter names to be consistent

    - The get_pvalue() method does not need the aMaxSize param

    - If the number of VCF columns for a particular line in a
      VCF does not equal the number of VCF header columns,
      then output a warning and skip the line.

aradenbaugh/radia