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Create a new column in serology mapping table that has the lgx version of the allele list lgx_allele_list 
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4 files changed

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‎pyard/ard.py‎

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@@ -123,6 +123,7 @@ def __init__(
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dr.generate_serology_mapping(
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self.db_connection, imgt_version, self.serology_mapping, self._redux_allele
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)
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# Load V2 to V3 mappings
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dr.generate_v2_to_v3_mapping(self.db_connection, imgt_version)
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# Save IMGT database version

‎pyard/drbx_tests.csv‎

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drb1,drb3,drb4,drb5
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HLA-DRB1*03:01+DRB1*04:01,DRB3*01:01,DRB4*01:03,
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HLA-DRB1*03:01+DRB1*04:01,DRB3*01:01+DRB3*02:01,DRB4*01:03,
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HLA-DRB1*03:01+DRB1*04:01,DRB3*01:01,DRB4*01:03+DRB4*01:05,
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HLA-DRB1*03:01+DRB1*04:01,DRB3*01:01,DRB4*01:03,DRB5*01:05
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HLA-DRB1*03:01+DRB1*04:01,,DRB4*01:03,
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HLA-DRB1*03:01+DRB1*04:01,DRB3*01:03,,
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HLA-DRB1*01:01+DRB1*08:01,,,
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HLA-DRB1*01:01+DRB1*08:01,DRB3*01:01,,
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HLA-DRB1*01:01+DRB1*08:01,,DRB4*01:01,
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HLA-DRB1*01:01+DRB1*08:01,,,DRB5*01:01
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HLA-DRB1*01:01+DRB1*03:01,DRB3*01:01,DRB4*01:03,,
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HLA-DRB1*01:01+DRB1*03:01,DRB3*01:01,,DRB5*01:03,
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HLA-DRB1*01:01+DRB1*03:01,,,,
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HLA-DRB1*01:01+DRB1*04:01,,DRB4*01:01+DRB4*01:03,
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HLA-DRB1*01:01+DRB1*04:01,DRB3*01:01,DRB4*01:03,
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HLA-DRB1*01:01+DRB1*04:01,,DRB4*01:01,DRB5*01:03
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HLA-DRB1*01:01+DRB1*04:01,,,,
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HLA-DRB1*03:01+DRB1*13:01,DRB3*01:01,,
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HLA-DRB1*03:01+DRB1*13:01,DRB3*01:01,DRB4*01:03,
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HLA-DRB1*03:01+DRB1*13:01,DRB3*01:01,,DRB5*01:03
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HLA-DRB1*03:01+DRB1*13:01,,DRB4*01:01,DRB5*01:03
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HLA-DRB1*04:01+DRB1*09:01,DRB3*01:01,,
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HLA-DRB1*04:01+DRB1*09:01,DRB3*01:01,DRB4*01:03,
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HLA-DRB1*04:01+DRB1*09:01,DRB3*01:01,,DRB5*01:03
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HLA-DRB1*15:01+DRB1*16:01,,DRB4*01:01,DRB5*01:03
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HLA-DRB1*15:01+DRB1*16:01,DRB3*01:01,,
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HLA-DRB1*15:01+DRB1*16:01,DRB3*01:01,DRB4*01:03,
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HLA-DRB1*15:01+DRB1*16:01,DRB3*01:01,,DRB5*01:03
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HLA-DRB1*15:01+DRB1*16:01,,DRB4*01:01,DRB5*01:03
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HLA-DRB1*15:01+DRB1*16:01,,,DRB5*01:03

‎pyard/serology.py‎

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valid_serology = {
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'A': ['A1', 'A2', 'A203', 'A210', 'A3', 'A9', 'A10', 'A11', 'A19', 'A23', 'A24', 'A2403', 'A25', 'A26', 'A28',
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'A29',
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'A30', 'A31', 'A32', 'A33', 'A34', 'A36', 'A43', 'A66', 'A68', 'A69', 'A74', 'A80'],
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'B': ['B5', 'B7', 'B703', 'B8', 'B12', 'B13', 'B14', 'B15', 'B16', 'B17', 'B18', 'B21', 'B22', 'B27', 'B2708',
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'B35',
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'B37', 'B38', 'B39', 'B3901', 'B3902', 'B40', 'B4005', 'B41', 'B42', 'B44', 'B45', 'B46', 'B47', 'B48', 'B49',
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'B50', 'B51', 'B5102', 'B5103', 'B52', 'B53', 'B54', 'B55', 'B56', 'B57', 'B58', 'B59', 'B60', 'B61', 'B62',
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'B63', 'B64', 'B65', 'B67', 'B70', 'B71', 'B72', 'B73', 'B75', 'B76', 'B77', 'B78', 'B81', 'B82', 'Bw4',
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'Bw6'],
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'C': ['Cw1', 'Cw2', 'Cw3', 'Cw4', 'Cw5', 'Cw6', 'Cw7', 'Cw8', 'Cw9', 'Cw10'],
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'D': ['Dw1', 'Dw2', 'Dw3', 'Dw4', 'Dw5', 'Dw6', 'Dw7', 'Dw8', 'Dw9', 'Dw10', 'Dw11', 'Dw12', 'Dw13', 'Dw14', 'Dw15',
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'Dw16', 'Dw17', 'Dw18', 'Dw19', 'Dw20', 'Dw21', 'Dw22', 'Dw23', 'Dw24', 'Dw25', 'Dw26'],
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'DR': ['DR1', 'DR103', 'DR2', 'DR3', 'DR4', 'DR5', 'DR6', 'DR7', 'DR8', 'DR9', 'DR10', 'DR11', 'DR12', 'DR13',
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'DR14',
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'DR1403', 'DR1404', 'DR15', 'DR16', 'DR17', 'DR18', 'DR51', 'DR52', 'DR53'],
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'DQ': ['DQ1', 'DQ2', 'DQ3', 'DQ4', 'DQ5', 'DQ6', 'DQ7', 'DQ8', 'DQ9'],
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'DP': ['DPw1', 'DPw2', 'DPw3', 'DPw4', 'DPw5', 'DPw6']
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}

‎pyard/valid_serology.json‎

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{
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"A": [
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"A1",
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"A2",
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"A203",
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"A210",
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"A3",
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"A9",
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"A10",
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"A11",
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"A19",
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"A23",
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"A24",
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"A2403",
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"A25",
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"A26",
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"A28",
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"A29",
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"A30",
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"A31",
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"A32",
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"A33",
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"A34",
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"A36",
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"A43",
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"A66",
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"A68",
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"A69",
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"A74",
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"A80"
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],
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"B": [
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"B5",
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"B7",
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"B703",
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"B8",
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"B12",
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"B13",
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"B14",
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"B15",
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"B16",
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"B17",
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"B18",
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"B21",
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"B22",
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"B27",
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"B2708",
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"B35",
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"B37",
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"B38",
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"B39",
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"B3901",
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"B3902",
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"B40",
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"B4005",
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"B41",
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"B42",
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"B44",
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"B45",
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"B46",
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"B47",
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"B48",
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"B49",
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"B50",
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"B51",
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"B5102",
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"B5103",
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"B52",
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"B53",
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"B54",
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"B55",
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"B56",
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"B57",
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"B58",
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"B59",
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"B60",
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"B61",
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"B62",
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"B63",
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"B64",
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"B65",
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"B67",
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"B70",
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"B71",
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"B72",
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"B73",
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"B75",
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"B76",
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"B77",
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"B78",
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"B81",
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"B82",
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"Bw4",
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"Bw6"
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],
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"C": [
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"Cw1",
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"Cw2",
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"Cw3",
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"Cw4",
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"Cw5",
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"Cw6",
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"Cw7",
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"Cw8",
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"Cw9",
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"Cw10"
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],
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"D": [
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"Dw1",
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"Dw2",
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"Dw3",
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"Dw4",
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"Dw5",
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"Dw6",
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"Dw7",
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"Dw8",
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"Dw9",
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"Dw10",
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"Dw11",
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"Dw12",
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"Dw13",
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"Dw14",
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"Dw15",
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"Dw16",
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"Dw17",
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"Dw18",
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"Dw19",
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"Dw20",
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"Dw21",
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"Dw22",
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"Dw23",
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"Dw24",
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"Dw25",
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"Dw26"
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],
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"DR": [
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"DR1",
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"DR103",
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"DR2",
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"DR3",
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"DR4",
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"DR5",
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"DR6",
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"DR7",
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"DR8",
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"DR9",
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"DR10",
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"DR11",
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"DR12",
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"DR13",
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"DR14",
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"DR1403",
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"DR1404",
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"DR15",
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"DR16",
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"DR17",
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"DR18",
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"DR51",
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"DR52",
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"DR53"
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],
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"DQ": [
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"DQ1",
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"DQ2",
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"DQ3",
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"DQ4",
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"DQ5",
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"DQ6",
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"DQ7",
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"DQ8",
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"DQ9"
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],
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"DP": [
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"DPw1",
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"DPw2",
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"DPw3",
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"DPw4",
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"DPw5",
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"DPw6"
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]
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}

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