service_config.h

#pragma once

#include <types.h>
#include <string>

namespace GLnexus {

enum class GLnexusOutputFormat {
    BCF,

    VCF,
};
struct genotyper_config {
    size_t required_dp = 0;

    std::string allele_dp_format = "AD";

    std::string ref_symbolic_allele = "<NON_REF>";

    std::string ref_dp_format = "MIN_DP";

    GLnexusOutputFormat output_format = GLnexusOutputFormat::BCF;

    // Should the genotyper write a record describing each call loss?
    // If true, the output is recorded in YAML format in the
    // [residuals_file].
    bool output_residuals = false;
    std::string residuals_file = "/tmp/residuals.yml";

    genotyper_config() = default;

    genotyper_config(GLnexusOutputFormat _output_format) : output_format(_output_format) {}
};

}