helios/bioruby-samtools — pull request #16 by danmaclean (2012-11-26 16:26:43+00:00)
Title: extra functionality!! 

Bio::DB::Pileup#to_vcf outputs a vcf string as per the samtools script
sam2vcf.pl (an older version of vcf). In cases where an indel is found,
the ref allele is represented as a *, since it is not practicable for
the reference fasta to be present.