hts_memory.h

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#ifndef __gamgee_hts_memory__
#define __gamgee_hts_memory__

#include "htslib/sam.h"
#include "htslib/vcf.h"

#include <memory>
#include <vector>
#include <string>

namespace gamgee {
namespace utils { 

struct HtsFileDeleter {
  void operator()(htsFile* p) const { hts_close(p); }
};

struct SamBodyDeleter {
  void operator()(bam1_t* p) const { bam_destroy1(p); }
};

struct SamHeaderDeleter {
  void operator()(bam_hdr_t* p) const { bam_hdr_destroy(p); }
};

struct VariantHeaderDeleter {
  void operator()(bcf_hdr_t* p) const { bcf_hdr_destroy(p); }
};

struct VariantBodyDeleter {
  void operator()(bcf1_t* p) const { bcf_destroy1(p); }
};

std::shared_ptr<bam1_t> make_shared_sam(bam1_t* sam_ptr);
std::shared_ptr<bam_hdr_t> make_shared_sam_header(bam_hdr_t* sam_header_ptr);
std::shared_ptr<bcf1_t> make_shared_variant(bcf1_t* bcf_ptr);
std::shared_ptr<bcf_hdr_t> make_shared_variant_header(bcf_hdr_t* bcf_hdr_ptr);

bam1_t* sam_deep_copy(bam1_t* original);
bam_hdr_t* sam_header_deep_copy(bam_hdr_t* original);
bcf1_t* variant_deep_copy(bcf1_t* original); 
bcf_hdr_t* variant_header_deep_copy(bcf_hdr_t* original);



}
}

#endif