hts_memory.h File Reference

#include "htslib/sam.h"
#include "htslib/vcf.h"
#include <memory>
#include <vector>
#include <string>

Go to the source code of this file.

Classes
struct	gamgee::utils::HtsFileDeleter
	a functor object to delete an htsFile pointer More...
struct	gamgee::utils::SamBodyDeleter
	a functor object to delete a bam1_t pointer More...
struct	gamgee::utils::SamHeaderDeleter
	a functor object to delete a bam_hdr_t pointer More...
struct	gamgee::utils::VariantHeaderDeleter
	a functor object to delete a bcf_hdr_t pointer More...
struct	gamgee::utils::VariantBodyDeleter
	a functor object to delete a bcf1_t pointer More...

Namespaces
	gamgee
	gamgee::utils
	utility functions for the gamgee library

Functions
shared_ptr< bam1_t >	gamgee::utils::make_shared_sam (bam1_t *sam_ptr)
	wraps a pre-allocated bam1_t in a shared_ptr with correct deleter More...
shared_ptr< bam_hdr_t >	gamgee::utils::make_shared_sam_header (bam_hdr_t *sam_header_ptr)
	wraps a pre-allocated bam_hdr_t in a shared_ptr with correct deleter More...
shared_ptr< bcf1_t >	gamgee::utils::make_shared_variant (bcf1_t *bcf_ptr)
	wraps a pre-allocated bcf1_t in a shared_ptr with correct deleter More...
shared_ptr< bcf_hdr_t >	gamgee::utils::make_shared_variant_header (bcf_hdr_t *bcf_hdr_ptr)
	wraps a pre-allocated bcf_hdr_t in a shared_ptr with correct deleter More...
bam1_t *	gamgee::utils::sam_deep_copy (bam1_t *original)
	creates a deep copy of an existing bam1_t More...
bam_hdr_t *	gamgee::utils::sam_header_deep_copy (bam_hdr_t *original)
	creates a deep copy of an existing bam_hdr_t More...
bcf1_t *	gamgee::utils::variant_deep_copy (bcf1_t *original)
	creates a deep copy of an existing bcf1_t More...
bcf_hdr_t *	gamgee::utils::variant_header_deep_copy (bcf_hdr_t *original)
	creates a deep copy of an existing bcf_hdr_t More...