class GffSNP

Public Instance Methods

report(snp, parent, seqid,n) click to toggle source
# File lib/gene_assembler/gff_snp.rb, line 2
def report(snp, parent, seqid,n)
        depth="Depth=#{snp.depth};"
        if snp.depth.nil?
                depth=nil
        end
        zygosity="Zygosity=#{snp.zygosity};"
        if snp.zygosity.nil?
                zygosity=nil 
        end
        mapping_qual="Mapping_qual=#{snp.mapping_qual};"
        if snp.mapping_qual.nil?
                mapping_qual=nil
        end
        strand_bias="Strand_bias=#{snp.strand_bias};"
                if snp.strand_bias.nil?
        end
        snp_text="#{seqid}\t#{snp.source}\tSNP\t#{snp.position}\t#{snp.position}\t.\t+\t.\tID=#{parent}_SNP_#{n};Parent=#{parent};Name=#{snp.ref} -> #{snp.var};Note=#{snp.ref} -> #{snp.var};#{depth}#{zygosity}#{mapping_qual}#{strand_bias}"
        return snp_text
end