variant_utils.h

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#ifndef gamgee__variant_utils__guard
#define gamgee__variant_utils__guard

#include "hts_memory.h"

#include "htslib/vcf.h"

#include <string>
#include <vector>

namespace gamgee {

void subset_variant_samples(bcf_hdr_t* hdr_ptr, const std::vector<std::string>& samples, const bool include);

enum class AlleleType { REFERENCE, SNP, INSERTION, DELETION };

using AlleleMask = std::vector<AlleleType>;

void merge_variant_headers(const std::shared_ptr<bcf_hdr_t>& dest_hdr_ptr, const std::shared_ptr<bcf_hdr_t>& src_hdr_ptr);
}

#endif /* gamgee__variant_utils__guard */