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Gamgee
You miserable little maggot. I'll stove your head in!
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Gamgee
You miserable little maggot. I'll stove your head in!
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#include "htslib/sam.h"#include "htslib/vcf.h"#include "htslib/synced_bcf_reader.h"#include "htslib/kstring.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::HtsIndexDeleter |
| a functor object to delete an hts file index pointer More... | |
| struct | gamgee::utils::HtsIteratorDeleter |
| a functor object to delete an hts file iterator 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... | |
| struct | gamgee::utils::SyncedReaderDeleter |
| a functor object to delete a bcf_srs_t pointer More... | |
Namespaces | |
| gamgee | |
| gamgee::utils | |
| utility functions for the gamgee library | |
Functions | |
| shared_ptr< htsFile > | gamgee::utils::make_shared_hts_file (htsFile *hts_file_ptr) |
| wraps a pre-allocated htsFile in a shared_ptr with correct deleter More... | |
| shared_ptr< hts_idx_t > | gamgee::utils::make_shared_hts_index (hts_idx_t *hts_index_ptr) |
| wraps a pre-allocated hts_idx_t in a shared_ptr with correct deleter More... | |
| shared_ptr< hts_itr_t > | gamgee::utils::make_shared_hts_itr (hts_itr_t *hts_itr_ptr) |
| wraps a pre-allocated hts_itr_t in a shared_ptr with correct deleter More... | |
| 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... | |
| std::shared_ptr< bcf_srs_t > | gamgee::utils::make_shared_synced_variant_reader (bcf_srs_t *synced_reader_ptr) |
| wraps a pre-allocated bcf_srs_t in a shared_ptr with correct deleter More... | |
| unique_ptr< htsFile, HtsFileDeleter > | gamgee::utils::make_unique_hts_file (htsFile *hts_file_ptr) |
| wraps a pre-allocated htsFile in a unique_ptr with correct deleter More... | |
| std::unique_ptr< hts_itr_t, HtsIteratorDeleter > | gamgee::utils::make_unique_hts_itr (hts_itr_t *hts_itr_ptr) |
| wraps a pre-allocated hts_itr_t in a unique_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... | |
| bam1_t * | gamgee::utils::sam_shallow_copy (bam1_t *original) |
| creates a shallow copy of an existing bam1_t: copies core fields but not the data buffer or fields related to the size of the data buffer More... | |
| std::string | gamgee::utils::htslib_filter_name (bcf_hdr_t *header, bcf1_t *body, int index) |
| helper function to translate an index into a string in the filter list More... | |
| uint8_t | gamgee::utils::bcf_type_to_element_size (const int32_t htslib_type) |
| Returns the number of bytes required to store each BCF_BT_* type. More... | |
| uint8_t | gamgee::utils::int_encoded_type (const int32_t val) |
| uint8_t | gamgee::utils::int_encoded_type (const int32_t min_val, const int32_t max_val) |
| Given a min and max value, determines whether int8, int16, or int32 BCF encoding is required. More... | |
| uint8_t | gamgee::utils::int_encoded_size (const int32_t val) |
| uint32_t | gamgee::utils::encoded_size (const int8_t field_type, const uint32_t field_length, bool add_type_descriptor=true) |
| kstring_t | gamgee::utils::initialize_htslib_buffer (const uint32_t initial_capacity) |
| Returns a newly-allocated kstring_t buffer suitable for passing to htslib. More... | |
1.8.8