module ViralSeq

  class TcsDr
    PARAMS = {:platform_error_rate=>0.02,
               :primer_pairs=>
                [{:region=>"RT",
                  :cdna=>
                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
                  :forward=>
                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
                  :majority=>0,
                  :end_join=>true,
                  :end_join_option=>1,
                  :overlap=>0,
                  :TCS_QC=>true,
                  :ref_genome=>"HXB2",
                  :ref_start=>2648,
                  :ref_end=>3257,
                  :indel=>true,
                  :trim=>false},
                 {:region=>"PR",
                  :cdna=>
                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
                  :forward=>
                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
                  :majority=>0,
                  :end_join=>true,
                  :end_join_option=>3,
                  :TCS_QC=>true,
                  :ref_genome=>"HXB2",
                  :ref_start=>0,
                  :ref_end=>2591,
                  :indel=>true,
                  :trim=>true,
                  :trim_ref=>"HXB2",
                  :trim_ref_start=>2253,
                  :trim_ref_end=>2549},
                 {:region=>"IN",
                  :cdna=>
                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC",
                  :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
                  :majority=>0,
                  :end_join=>true,
                  :end_join_option=>2,
                  :overlap=>171,
                  :TCS_QC=>true,
                  :ref_genome=>"HXB2",
                  :ref_start=>4384,
                  :ref_end=>4751,
                  :indel=>false,
                  :trim=>false},
                 {:region=>"V1V3",
                  :cdna=>
                   "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
                  :forward=>
                   "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
                  :majority=>0,
                  :end_join=>true,
                  :end_join_option=>1,
                  :overlap=>0,
                  :TCS_QC=>true,
                  :ref_genome=>"HXB2",
                  :ref_start=>6585,
                  :ref_end=>7205..7210,
                  :indel=>true,
                  :trim=>false},
                  {:region=>"P17",
                   :cdna=>
                    "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
                   :forward=>
                    "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
                   :majority=>0,
                   :end_join=>true,
                   :end_join_option=>1,
                   :overlap=>0,
                   :TCS_QC=>true,
                   :ref_genome=>"HXB2",
                   :ref_start=>1196,
                   :ref_end=>1725,
                   :indel=>true,
                   :trim=>false}
                  ]
              }
  end

end