from collections import namedtuple

# GENOMIC VERSION:
VERSION = "hg38" # equivalent to GRCh38

# Specific columns in the output matrix
COLUMN_SOURCE = 0
COLUMN_GENE = 1
COLUMN_GENOMIC_HGVS = 2
COLUMN_VCF_CHR = 3
COLUMN_VCF_POS = 4
COLUMN_VCF_REF = 5
COLUMN_VCF_ALT = 6

# This is the string to be stored when a field is empty
DEFAULT_CONTENTS = "-"

# key value pair dictionaries of all extra fields in various databases to add
GENOME1K_FIELDS = {"Allele_frequency": "AF",
                   "EAS_Allele_frequency": "EAS_AF",
                   "EUR_Allele_frequency": "EUR_AF",
                   "AFR_Allele_frequency": "AFR_AF",
                   "AMR_Allele_frequency": "AMR_AF",
                   "SAS_Allele_frequency": "SAS_AF",
                   "BX_ID": "BX_ID"}

CLINVAR_FIELDS = {"HGVS": "HGVS",
                  "Submitter": "Submitter",
                  "Clinical_Significance": "ClinicalSignificance",
                  "Date_Last_Updated": "DateLastUpdated",
                  "DateSignificanceLastEvaluated":
                      "DateSignificanceLastEvaluated",
                  "SCV": "SCV",
                  "SCV_Version": "SCV_Version",
                  "Allele_Origin": "Origin",
                  "Protein": "Protein",
                  "Method": "Method",
                  "Description": "Description",
                  "Review_Status": "ReviewStatus",
                  "Synonyms": "Synonyms",
                  "Summary_Evidence": "SummaryEvidence",
                  "Condition_Type": "ConditionType",
                  "Condition_Value": "ConditionValue",
                  "Condition_DB_ID": "ConditionDB_ID",
                  "BX_ID": "BX_ID"}

LOVD_FIELDS = {"Variant_frequency": "frequency",
               "Remarks": "remarks",
               "Classification": "classification",
               "HGVS_cDNA": "cDNA",
               "HGVS_protein": "Protein",
               "Genetic_origin": "genetic_origin",
               "RNA": "RNA",
               "Variant_effect": "variant_effect",
               "Individuals": "individuals",
               "Submitters": "submitters",
               "DBID": "DBID",
               "BX_ID": "BX_ID",
               "Created_date": "created_date",
               "Edited_date": "edited_date",
               "Submission_ID": "submission_id"
               }

EX_LOVD_FIELDS = {"Combined_prior_probablility": "combined_prior_p",
                  "Segregation_LR": "segregation_lr",
                  "Sum_family_LR": "sum_family_lr",
                  "Co_occurrence_LR": "co_occurrence_lr",
                  "Case_control_LR": "case_control_lr",
                  "Pathology_LR": "pathology_lr",
                  "Missense_analysis_prior_probability": "missense_analysis_prior_p",
                  "Posterior_probability": "posterior_p",
                  "IARC_class": "iarc_class",
                  "BIC_Nomenclature": "bic_dna_change",
                  "Literature_source": "key_observational_reference",
                  "HGVS_cDNA": "dna_change",
                  "HGVS_protein": "protein_change",
                  "BX_ID": "BX_ID"}

BIC_FIELDS = {"Clinical_classification": "Category",
              "Number_of_family_member_carrying_mutation": "Number_Reported",
              "Patient_nationality": "Nationality",
              "Germline_or_Somatic": "G_or_S",
              "Mutation_type": "Mutation_Type",
              "BIC_Designation": "Designation",
              "Clinical_importance": "Clinically_Importance",
              "Ethnicity": "Ethnicity",
              "Literature_citation": "Reference",
              "BX_ID": "BX_ID"}

ESP_FIELDS = {"polyPhen2_result": "PH",
              "Minor_allele_frequency_percent": "MAF",
              "EA_Allele_Frequency": "BX_EAAF",
              "AA_Allele_Frequency": "BX_AAAF",
              "Allele_Frequency": "BX_AF",
              "BX_ID": "BX_ID"}


EXAC_FIELDS = {"Allele_frequency": "AF",
               "Allele_count_AFR": "AC_AFR",
               "Allele_number_AFR": "AN_AFR",
               "Allele_frequency_AFR": "AF_AFR",
               "Homozygous_count_AFR": "Hom_AFR",
               "Allele_count_AMR": "AC_AMR",
               "Allele_number_AMR": "AN_AMR",
               "Allele_frequency_AMR": "AF_AMR",
               "Homozygous_count_AMR": "Hom_AMR",
               "Allele_count_EAS": "AC_EAS",
               "Allele_number_EAS": "AN_EAS",
               "Allele_frequency_EAS": "AF_EAS",
               "Homozygous_count_EAS": "Hom_EAS",
               "Allele_count_FIN": "AC_FIN",
               "Allele_number_FIN": "AN_FIN",
               "Allele_frequency_FIN": "AF_FIN",
               "Homozygous_count_FIN": "Hom_FIN",
               "Allele_count_NFE": "AC_NFE",
               "Allele_number_NFE": "AN_NFE",
               "Allele_frequency_NFE": "AF_NFE",
               "Homozygous_count_NFE": "Hom_NFE",
               "Allele_count_OTH": "AC_OTH",
               "Allele_number_OTH": "AN_OTH",
               "Allele_frequency_OTH": "AF_OTH",
               "Homozygous_count_OTH": "Hom_OTH",
               "Allele_count_SAS": "AC_SAS",
               "Allele_number_SAS": "AN_SAS",
               "Allele_frequency_SAS": "AF_SAS",
               "Homozygous_count_SAS": "Hom_SAS",
               "BX_ID": "BX_ID"}

EXAC_SUBPOPULATIONS = ["AFR", "AMR", "EAS", "FIN", "NFE", "OTH", "SAS"]

GNOMAD_V2_FIELDS = {"HGVS_cDNA": "hgvs",
                 "Flags": "flags",
                 "Variant_id": "variantId",

                 "faf95_popmax_genome": "genome_popmax",
                 "faf95_popmax_population_genome": "genome_popmax_population",

                 "Allele_count_genome_AFR": "genome_AFR_ac",
                 "Allele_count_hom_genome_AFR": "genome_AFR_ac_hom",
                 "Allele_number_genome_AFR": "genome_AFR_an",
                 "Allele_frequency_genome_AFR": "genome_AFR_af",

                 "Allele_count_genome_AMR": "genome_AMR_ac",
                 "Allele_count_hom_genome_AMR": "genome_AMR_ac_hom",
                 "Allele_number_genome_AMR": "genome_AMR_an",
                 "Allele_frequency_genome_AMR": "genome_AMR_af",

                 "Allele_count_genome_ASJ": "genome_ASJ_ac",
                 "Allele_count_hom_genome_ASJ": "genome_ASJ_ac_hom",
                 "Allele_number_genome_ASJ": "genome_ASJ_an",
                 "Allele_frequency_genome_ASJ": "genome_ASJ_af",

                 "Allele_count_genome_EAS": "genome_EAS_ac",
                 "Allele_count_hom_genome_EAS": "genome_EAS_ac_hom",
                 "Allele_number_genome_EAS": "genome_EAS_an",
                 "Allele_frequency_genome_EAS": "genome_EAS_af",

                 "Allele_count_genome_EAS_JPN": "genome_EAS_JPN_ac",
                 "Allele_count_hom_genome_EAS_JPN": "genome_EAS_JPN_ac_hom",
                 "Allele_number_genome_EAS_JPN": "genome_EAS_JPN_an",
                 "Allele_frequency_genome_EAS_JPN": "genome_EAS_JPN_af",

                 "Allele_count_genome_EAS_KOR": "genome_EAS_KOR_ac",
                 "Allele_count_hom_genome_EAS_KOR": "genome_EAS_KOR_ac_hom",
                 "Allele_number_genome_EAS_KOR": "genome_EAS_KOR_an",
                 "Allele_frequency_genome_EAS_KOR": "genome_EAS_KOR_af",

                 "Allele_count_genome_EAS_OEA": "genome_EAS_OEA_ac",
                 "Allele_count_hom_genome_EAS_OEA": "genome_EAS_OEA_ac_hom",
                 "Allele_number_genome_EAS_OEA": "genome_EAS_OEA_an",
                 "Allele_frequency_genome_EAS_OEA": "genome_EAS_OEA_af",

                 "Allele_count_genome_FIN": "genome_FIN_ac",
                 "Allele_count_hom_genome_FIN": "genome_FIN_ac_hom",
                 "Allele_number_genome_FIN": "genome_FIN_an",
                 "Allele_frequency_genome_FIN": "genome_FIN_af",

                 "Allele_count_genome_NFE": "genome_NFE_ac",
                 "Allele_count_hom_genome_NFE": "genome_NFE_ac_hom",
                 "Allele_number_genome_NFE": "genome_NFE_an",
                 "Allele_frequency_genome_NFE": "genome_NFE_af",

                 "Allele_count_genome_NFE_EST": "genome_NFE_EST_ac",
                 "Allele_count_hom_genome_NFE_EST": "genome_NFE_EST_ac_hom",
                 "Allele_number_genome_NFE_EST": "genome_NFE_EST_an",
                 "Allele_frequency_genome_NFE_EST": "genome_NFE_EST_af",

                 "Allele_count_genome_NFE_BGR": "genome_NFE_BGR_ac",
                 "Allele_count_hom_genome_NFE_BGR": "genome_NFE_BGR_ac_hom",
                 "Allele_number_genome_NFE_BGR": "genome_NFE_BGR_an",
                 "Allele_frequency_genome_NFE_BGR": "genome_NFE_BGR_af",

                 "Allele_count_genome_NFE_NWE": "genome_NFE_NWE_ac",
                 "Allele_count_hom_genome_NFE_NWE": "genome_NFE_NWE_ac_hom",
                 "Allele_number_genome_NFE_NWE": "genome_NFE_NWE_an",
                 "Allele_frequency_genome_NFE_NWE": "genome_NFE_NWE_af",

                 "Allele_count_genome_NFE_ONF": "genome_NFE_ONF_ac",
                 "Allele_count_hom_genome_NFE_ONF": "genome_NFE_ONF_ac_hom",
                 "Allele_number_genome_NFE_ONF": "genome_NFE_ONF_an",
                 "Allele_frequency_genome_NFE_ONF": "genome_NFE_ONF_af",

                 "Allele_count_genome_NFE_SEU": "genome_NFE_SEU_ac",
                 "Allele_count_hom_genome_NFE_SEU": "genome_NFE_SEU_ac_hom",
                 "Allele_number_genome_NFE_SEU": "genome_NFE_SEU_an",
                 "Allele_frequency_genome_NFE_SEU": "genome_NFE_SEU_af",

                 "Allele_count_genome_NFE_SWE": "genome_NFE_SWE_ac",
                 "Allele_count_hom_genome_NFE_SWE": "genome_NFE_SWE_ac_hom",
                 "Allele_number_genome_NFE_SWE": "genome_NFE_SWE_an",
                 "Allele_frequency_genome_NFE_SWE": "genome_NFE_SWE_af",

                 "Allele_count_genome_OTH": "genome_OTH_ac",
                 "Allele_count_hom_genome_OTH": "genome_OTH_ac_hom",
                 "Allele_number_genome_OTH": "genome_OTH_an",
                 "Allele_frequency_genome_OTH": "genome_OTH_af",

                 "Allele_count_genome_SAS": "genome_SAS_ac",
                 "Allele_count_hom_genome_SAS": "genome_SAS_ac_hom",
                 "Allele_number_genome_SAS": "genome_SAS_an",
                 "Allele_frequency_genome_SAS": "genome_SAS_af",

                 "Allele_count_genome": "genome_ac",
                 "Allele_number_genome": "genome_an",
                 "Allele_frequency_genome": "genome_af",

                 "faf95_popmax_exome": "exome_popmax",
                 "faf95_popmax_population_exome": "exome_popmax_population",

                 "Allele_count_exome_AFR": "exome_AFR_ac",
                 "Allele_count_hom_exome_AFR": "exome_AFR_ac_hom",
                 "Allele_number_exome_AFR": "exome_AFR_an",
                 "Allele_frequency_exome_AFR": "exome_AFR_af",

                 "Allele_count_exome_AMR": "exome_AMR_ac",
                 "Allele_count_hom_exome_AMR": "exome_AMR_ac_hom",
                 "Allele_number_exome_AMR": "exome_AMR_an",
                 "Allele_frequency_exome_AMR": "exome_AMR_af",

                 "Allele_count_exome_ASJ": "exome_ASJ_ac",
                 "Allele_count_hom_exome_ASJ": "exome_ASJ_ac_hom",
                 "Allele_number_exome_ASJ": "exome_ASJ_an",
                 "Allele_frequency_exome_ASJ": "exome_ASJ_af",

                 "Allele_count_exome_EAS": "exome_EAS_ac",
                 "Allele_count_hom_exome_EAS": "exome_EAS_ac_hom",
                 "Allele_number_exome_EAS": "exome_EAS_an",
                 "Allele_frequency_exome_EAS": "exome_EAS_af",

                 "Allele_count_exome_EAS_JPN": "exome_EAS_JPN_ac",
                 "Allele_count_hom_exome_EAS_JPN": "exome_EAS_JPN_ac_hom",
                 "Allele_number_exome_EAS_JPN": "exome_EAS_JPN_an",
                 "Allele_frequency_exome_EAS_JPN": "exome_EAS_JPN_af",

                 "Allele_count_exome_EAS_KOR": "exome_EAS_KOR_ac",
                 "Allele_count_hom_exome_EAS_KOR": "exome_EAS_KOR_ac_hom",
                 "Allele_number_exome_EAS_KOR": "exome_EAS_KOR_an",
                 "Allele_frequency_exome_EAS_KOR": "exome_EAS_KOR_af",

                 "Allele_count_exome_EAS_OEA": "exome_EAS_OEA_ac",
                 "Allele_count_hom_exome_EAS_OEA": "exome_EAS_OEA_ac_hom",
                 "Allele_number_exome_EAS_OEA": "exome_EAS_OEA_an",
                 "Allele_frequency_exome_EAS_OEA": "exome_EAS_OEA_af",

                 "Allele_count_exome_FIN": "exome_FIN_ac",
                 "Allele_count_hom_exome_FIN": "exome_FIN_ac_hom",
                 "Allele_number_exome_FIN": "exome_FIN_an",
                 "Allele_frequency_exome_FIN": "exome_FIN_af",

                 "Allele_count_exome_NFE": "exome_NFE_ac",
                 "Allele_count_hom_exome_NFE": "exome_NFE_ac_hom",
                 "Allele_number_exome_NFE": "exome_NFE_an",
                 "Allele_frequency_exome_NFE": "exome_NFE_af",

                 "Allele_count_exome_NFE_EST": "exome_NFE_EST_ac",
                 "Allele_count_hom_exome_NFE_EST": "exome_NFE_EST_ac_hom",
                 "Allele_number_exome_NFE_EST": "exome_NFE_EST_an",
                 "Allele_frequency_exome_NFE_EST": "exome_NFE_EST_af",

                 "Allele_count_exome_NFE_BGR": "exome_NFE_BGR_ac",
                 "Allele_count_hom_exome_NFE_BGR": "exome_NFE_BGR_ac_hom",
                 "Allele_number_exome_NFE_BGR": "exome_NFE_BGR_an",
                 "Allele_frequency_exome_NFE_BGR": "exome_NFE_BGR_af",

                 "Allele_count_exome_NFE_NWE": "exome_NFE_NWE_ac",
                 "Allele_count_hom_exome_NFE_NWE": "exome_NFE_NWE_ac_hom",
                 "Allele_number_exome_NFE_NWE": "exome_NFE_NWE_an",
                 "Allele_frequency_exome_NFE_NWE": "exome_NFE_NWE_af",

                 "Allele_count_exome_NFE_ONF": "exome_NFE_ONF_ac",
                 "Allele_count_hom_exome_NFE_ONF": "exome_NFE_ONF_ac_hom",
                 "Allele_number_exome_NFE_ONF": "exome_NFE_ONF_an",
                 "Allele_frequency_exome_NFE_ONF": "exome_NFE_ONF_af",

                 "Allele_count_exome_NFE_SEU": "exome_NFE_SEU_ac",
                 "Allele_count_hom_exome_NFE_SEU": "exome_NFE_SEU_ac_hom",
                 "Allele_number_exome_NFE_SEU": "exome_NFE_SEU_an",
                 "Allele_frequency_exome_NFE_SEU": "exome_NFE_SEU_af",

                 "Allele_count_exome_NFE_SWE": "exome_NFE_SWE_ac",
                 "Allele_count_hom_exome_NFE_SWE": "exome_NFE_SWE_ac_hom",
                 "Allele_number_exome_NFE_SWE": "exome_NFE_SWE_an",
                 "Allele_frequency_exome_NFE_SWE": "exome_NFE_SWE_af",

                 "Allele_count_exome_OTH": "exome_OTH_ac",
                 "Allele_count_hom_exome_OTH": "exome_OTH_ac_hom",
                 "Allele_number_exome_OTH": "exome_OTH_an",
                 "Allele_frequency_exome_OTH": "exome_OTH_af",

                 "Allele_count_exome_SAS": "exome_SAS_ac",
                 "Allele_count_hom_exome_SAS": "exome_SAS_ac_hom",
                 "Allele_number_exome_SAS": "exome_SAS_an",
                 "Allele_frequency_exome_SAS": "exome_SAS_af",

                 "Allele_number_exome": "exome_an",
                 "Allele_count_exome": "exome_ac",
                 "Allele_frequency_exome": "exome_af",

                 "BX_ID": "BX_ID"}


GNOMAD_V2_SUBPOPULATIONS = ["AFR", "AMR", "ASJ", "EAS", "EAS_JPN", "EAS_KOR", "EAS_OEA",
                         "FIN", "NFE", "NFE_EST", "NFE_BGR", "NFE_NWE", "NFE_ONF",
                         "NFE_SEU", "NFE_SWE", "OTH", "SAS"]

GNOMAD_V3_FIELDS = {"HGVS_cDNA": "hgvs",
                 "Flags": "flags",
                 "Variant_id": "variant_id",

                 "faf95_popmax_genome": "genome_popmax",
                 "faf95_popmax_population_genome": "genome_popmax_population",

                 "Allele_count_genome_AFR": "genome_AFR_ac",
                 "Allele_count_hom_genome_AFR": "genome_AFR_ac_hom",
                 "Allele_number_genome_AFR": "genome_AFR_an",
                 "Allele_frequency_genome_AFR": "genome_AFR_af",

                 "Allele_count_genome_AMR": "genome_AMR_ac",
                 "Allele_count_hom_genome_AMR": "genome_AMR_ac_hom",
                 "Allele_number_genome_AMR": "genome_AMR_an",
                 "Allele_frequency_genome_AMR": "genome_AMR_af",

                 "Allele_count_genome_ASJ": "genome_ASJ_ac",
                 "Allele_count_hom_genome_ASJ": "genome_ASJ_ac_hom",
                 "Allele_number_genome_ASJ": "genome_ASJ_an",
                 "Allele_frequency_genome_ASJ": "genome_ASJ_af",

                 "Allele_count_genome_EAS": "genome_EAS_ac",
                 "Allele_count_hom_genome_EAS": "genome_EAS_ac_hom",
                 "Allele_number_genome_EAS": "genome_EAS_an",
                 "Allele_frequency_genome_EAS": "genome_EAS_af",

                 "Allele_count_genome_FIN": "genome_FIN_ac",
                 "Allele_count_hom_genome_FIN": "genome_FIN_ac_hom",
                 "Allele_number_genome_FIN": "genome_FIN_an",
                 "Allele_frequency_genome_FIN": "genome_FIN_af",

                 "Allele_count_genome_NFE": "genome_NFE_ac",
                 "Allele_count_hom_genome_NFE": "genome_NFE_ac_hom",
                 "Allele_number_genome_NFE": "genome_NFE_an",
                 "Allele_frequency_genome_NFE": "genome_NFE_af",

                 "Allele_count_genome_OTH": "genome_OTH_ac",
                 "Allele_count_hom_genome_OTH": "genome_OTH_ac_hom",
                 "Allele_number_genome_OTH": "genome_OTH_an",
                 "Allele_frequency_genome_OTH": "genome_OTH_af",

                 "Allele_count_genome_SAS": "genome_SAS_ac",
                 "Allele_count_hom_genome_SAS": "genome_SAS_ac_hom",
                 "Allele_number_genome_SAS": "genome_SAS_an",
                 "Allele_frequency_genome_SAS": "genome_SAS_af",

                 "Allele_count_genome_MID": "genome_MID_ac",
                 "Allele_count_hom_genome_MID": "genome_MID_ac_hom",
                 "Allele_number_genome_MID": "genome_MID_an",
                 "Allele_frequency_genome_MID": "genome_MID_af",

                 "Allele_count_genome_AMI": "genome_AMI_ac",
                 "Allele_count_hom_genome_AMI": "genome_AMI_ac_hom",
                 "Allele_number_genome_AMI": "genome_AMI_an",
                 "Allele_frequency_genome_AMI": "genome_AMI_af",

                 "Allele_count_genome": "genome_ac",
                 "Allele_number_genome": "genome_an",
                 "Allele_frequency_genome": "genome_af",

                 "BX_ID": "BX_ID"}


GNOMAD_V3_SUBPOPULATIONS = ["AFR", "AMR", "ASJ", "EAS", "FIN", "NFE",
                            "OTH", "SAS", "MID", "AMI"]

ENIGMA_BRCA12_FUNCTIONAL_ASSAY_SCORES_FIELDS = {
              "HGVS_Nucleotide": "HGVS_Nucleotide_Variant",
              "Chromosomal_Variant": "Chromosomal_Variant",
              "Result_Findlay": "Result_Findlay",
              "Functional_Enrichment_Score_Findlay": "Function_Score_Findlay",
              "RNA_Score_Findlay": "RNA_Score_Findlay",
              "RNA_Class_Findlay": "RNA_Class_Findlay",
              "Result_Starita": "Result_Starita",
              "Control_Group_Petitalot": "Control_Group_Petitalot",
              "Result_Petitalot": "Result_Petitalot",
              "Selection_Bouwman1": "Selection_Bouwman1",
              "Result_Bouwman1": "Result_Bouwman1",
              "Cisplatin_Bouwman2": "Cisplatin_Bouwman2",
              "Olaparib_Bouwman2": "Olaparib_Bouwman2",
              "DRGFP_Bouwman2": "DRGFP_Bouwman2",
              "Result_Bouwman2": "Result_Bouwman2",
              "Result_Fernandes": "Result_Fernandes",
              "Complementation_Mesman": "Complementation_Mesman",
              "HDR_Mesman": "HDR_Mesman",
              "Cisplatin_Mesman": "Cisplatin_Mesman",
              "Result_Mesman": "Result_Mesman",
              "HDR_Richardson": "HDR_Richardson",
              "Result_Richardson": "Result_Richardson",
              "Result_Ikegami": "Result_Ikegami",
              "Olaparib_fClass_Ikegami": "Olaparib_fClass_Ikegami",
              "Niraparif_fClass_Ikegami": "Niraparif_fClass_Ikegami",
              "Rucaparib_fClass_Ikegami": "Rucaparib_fClass_Ikegami",
              "CBDCA_fClass_Ikegami": "CBDCA_fClass_Ikegami",
              "Cell_Survival_Biwas": "HAT_(Cell_Survival)_Biwas",
              "Drug_Sensitivity_Biwas": "DS_(Drug_Sensitivity)_Biwas",
              "HAT_DS_Score_Biwas": "HAT+DS_Score_Biwas",
              "Result_Biwas": "Result_Biwas",
              "BX_ID": "BX_ID"
}

FIELD_DICT = {"1000_Genomes": GENOME1K_FIELDS,
              "ClinVar": CLINVAR_FIELDS,
              "LOVD": LOVD_FIELDS,
              "exLOVD": EX_LOVD_FIELDS,
              "ExAC": EXAC_FIELDS,
              "ESP": ESP_FIELDS,
              "BIC": BIC_FIELDS,
              "GnomAD": GNOMAD_V2_FIELDS,
              "GnomADv3": GNOMAD_V3_FIELDS,
              "ENIGMA_BRCA12_Functional_Assays": ENIGMA_BRCA12_FUNCTIONAL_ASSAY_SCORES_FIELDS}

LIST_TYPE_FIELDS = {
    "SCV", # Clinvar, treating it as list, to have the same order as with SCV_Version
    "SCV_Version"
}

ENIGMA_FILE = "enigma_from_clinvar.tsv"

GENOME1K_FILE = "1000G.sorted.hg38.vcf"
CLINVAR_FILE = "ClinVar.vcf"
LOVD_FILE = "sharedLOVD.sorted.hg38.vcf"
EX_LOVD_FILE = "exLOVD_brca12.sorted.hg38.vcf"
BIC_FILE = "bic_brca12.sorted.hg38.vcf"
EXAC_FILE = "exac.brca12.sorted.hg38.vcf"
ESP_FILE = "esp.sorted.hg38.vcf"
GNOMAD_V2_FILE = "gnomADv2.sorted.hg38.vcf"
GNOMAD_V3_FILE = "gnomADv3.sorted.hg38.vcf"

# Functional Assays
FUNCTIONAL_ASSAYS_SCORES_FILE = "ENIGMA_BRCA12_functional_assays_scores.sorted.hg38.vcf"

VCFVariant = namedtuple("VCFVariant", "chr,pos,ref,alt")
