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#ifndef THIRD_PARTY_NUCLEUS_IO_MERGE_VARIANTS_H_
#define THIRD_PARTY_NUCLEUS_IO_MERGE_VARIANTS_H_

#include "third_party/nucleus/io/reference.h"
#include "third_party/nucleus/io/variant_reader.h"
#include "third_party/nucleus/io/vcf_writer.h"
namespace nucleus {

using nucleus::genomics::v1::Variant;

std::unique_ptr<Variant> CreateRecordFromTemplate(const Variant& t, int start,
                                                  int end,
                                                  const GenomeReference& ref);

// Modifies a variant to include gVCF allele and associated likelihoods.
//
// Modifies the given variant by applying the modification to its alleles and
//    allele-related FORMAT fields.
void TransfromToGvcf(Variant* variant);

// Zero-scales GL to mimic write-then-read.
//
// When writing variants using VcfWriter, GLs are converted to PLs, which is an
// integer format scaled so the most likely genotype has value 0. This function
// modifies the input variant to mimic this transformation of GL -> PL -> GL.
void ZeroScaleGl(Variant* variant);

void MergeAndWriteVariantsAndNonVariants(
    bool only_keep_pass, const std::string& variant_file_path,
    const std::vector<std::string>& non_variant_file_paths,
    const std::string& fasta_path, const std::string& vcf_out_path,
    const std::string& gvcf_out_path,
    const nucleus::genomics::v1::VcfHeader& header,
    bool process_somatic = false);

void MergeAndWriteVariantsAndNonVariants(
    bool only_keep_pass, VariantReader* variant_reader,
    ShardedVariantReader* non_variant_reader, VcfWriter* vcf_writer,
    VcfWriter* gvcf_writer, const GenomeReference& ref,
    bool process_somatic = false);

}  // namespace nucleus

#endif  // THIRD_PARTY_NUCLEUS_IO_MERGE_VARIANTS_H_