Outputting vcf file of all the spiked in variants from SomaticSpike.
Added vcf header initialization.
Changing parameters to match the new usage.
-- -V, the input vcf file is now required
-- -vout, the output vcf file is now required
-- --spiked_intervals_out is now optional
Edited GenerateBenchmark.scala to match the changes to SomaticSpike.