Added DP4 field
Added DP4 field

    - Added DP4 field:  The 'Number' field in the header
      for 'DP4' should be '4' and the VCF lines should
      only specify the ref-forward, ref-reverse,
      alt-forward and alt-reverse values of the passing
      call, but we are allowing an unspecified number
      of values for the 'DP4' field.  The initial RADIA
      script outputs variants at very low depth and
      frequency, which results in many calls with multiple
      alleles.  Before filtering, it is impossible to know
      which alternative allele will be part of the final
      passing call when multiple alleles are present.
      During the filtering process, we know which alternative
      allele to choose from the passing call and could limit
      the values at that point, but for all non-passing calls,
      we would need to choose an arbitrary alternative allele
      to limit it to just 4 values.  In order to provide the
      most complete information, all forward and reverse values
      for all alleles is provided in the specified order.
      This makes it easy to extract the final alt-forward and
      alt-reverse values for any alternative allele.

    - Added newline after p-value header line

    - Changed the 'Number' for several INFO
      and FORMAT fields from the generic '.'
      to 'A' for all alternative alleles and
      'R' for all alleles including the
      reference.

aradenbaugh/radia