def to_oncotator(self):
        """Returns mutation in oncotator input format. Assumes mutations have
        vcf/mpileup style positions."""
        if self.type == ".":
            ref = self.ref
            alt = self.change
            start = self.pos
            end = self.pos
        elif self.type == "-":
            ref = self.change
            alt = "-"
            start = self.pos + 1
            end = start + len(self.change)
        elif self.type == "+":
            ref = "-"
            alt = self.change
            start = self.pos
            end = start + len(self.change)
        else:
            raise(Exception("Unexpected mutation type: {}".format(self.type)))
        return "{chrom}\t{start}\t{end}\t{ref}\t{alt}".format(chrom=self.chrom, start=start,
                                                            end=end, ref=ref, alt=alt)
def to_oncotator ( self ) : if self . type == "." : ref = self . ref alt = self . change start = self . pos end = self . pos elif self . type == "-" : ref = self . change alt = "-" start = self . pos + 1 end = start + len ( self . change ) elif self . type == "+" : ref = "-" alt = self . change start = self . pos end = start + len ( self . change ) else : raise ( Exception ( "Unexpected mutation type: {}" . format ( self . type ) ) ) return "{chrom}\t{start}\t{end}\t{ref}\t{alt}" . format ( chrom = self . chrom , start = start , end = end , ref = ref , alt = alt )
Returns mutation in oncotator input format. Assumes mutations have
        vcf/mpileup style positions.