Detailed description

Definition at line 195 of file cram_structs.h.

#include <cram_structs.h>

Public Methods
	khash_t (m_s2i)*TD_hash

	khash_t (map)*preservation_map

Public Members
int32_t	ref_seq_id

int32_t	ref_seq_start

int32_t	ref_seq_span

int32_t	num_records

int32_t	num_landmarks

int32_t *	landmark

int	mapped_qs_included

int	unmapped_qs_included

int	unmapped_placed

int	qs_included

int	read_names_included

int	AP_delta

char	substitution_matrix [5][4]

cram_block *	TD_blk

int	nTL

unsigned char **	TL

string_alloc_t *	TD_keys

struct cram_map *	rec_encoding_map [CRAM_MAP_HASH]

struct cram_map *	tag_encoding_map [CRAM_MAP_HASH]

struct cram_codec *	BF_codec

struct cram_codec *	CF_codec

struct cram_codec *	RL_codec

struct cram_codec *	AP_codec

struct cram_codec *	RG_codec

struct cram_codec *	MF_codec

struct cram_codec *	NS_codec

struct cram_codec *	NP_codec

struct cram_codec *	TS_codec

struct cram_codec *	NF_codec

struct cram_codec *	TC_codec

struct cram_codec *	TN_codec

struct cram_codec *	TL_codec

struct cram_codec *	FN_codec

struct cram_codec *	FC_codec

struct cram_codec *	FP_codec

struct cram_codec *	BS_codec

struct cram_codec *	IN_codec

struct cram_codec *	SC_codec

struct cram_codec *	DL_codec

struct cram_codec *	BA_codec

struct cram_codec *	RS_codec

struct cram_codec *	PD_codec

struct cram_codec *	HC_codec

struct cram_codec *	MQ_codec

struct cram_codec *	RN_codec

struct cram_codec *	QS_codec

struct cram_codec *	Qs_codec

struct cram_codec *	RI_codec

struct cram_codec *	TM_codec

struct cram_codec *	TV_codec

char *	uncomp

size_t	uncomp_size

size_t	uncomp_alloc

Member Function Documentation

cram_block_compression_hdr::khash_t ( m_s2i )

cram_block_compression_hdr::khash_t ( map )

Member Data Documentation

struct cram_codec* cram_block_compression_hdr::AP_codec

Definition at line 227 of file cram_structs.h.

int cram_block_compression_hdr::AP_delta

Definition at line 209 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::BA_codec

Definition at line 244 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::BF_codec

Definition at line 224 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::BS_codec

Definition at line 240 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::CF_codec

Definition at line 225 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::DL_codec

Definition at line 243 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::FC_codec

Definition at line 238 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::FN_codec

Definition at line 237 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::FP_codec

Definition at line 239 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::HC_codec

Definition at line 247 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::IN_codec

Definition at line 241 of file cram_structs.h.

int32_t* cram_block_compression_hdr::landmark

Definition at line 201 of file cram_structs.h.

int cram_block_compression_hdr::mapped_qs_included

Definition at line 204 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::MF_codec

Definition at line 229 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::MQ_codec

Definition at line 248 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::NF_codec

Definition at line 233 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::NP_codec

Definition at line 231 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::NS_codec

Definition at line 230 of file cram_structs.h.

int cram_block_compression_hdr::nTL

Definition at line 215 of file cram_structs.h.

int32_t cram_block_compression_hdr::num_landmarks

Definition at line 200 of file cram_structs.h.

int32_t cram_block_compression_hdr::num_records

Definition at line 199 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::PD_codec

Definition at line 246 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::QS_codec

Definition at line 250 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::Qs_codec

Definition at line 251 of file cram_structs.h.

int cram_block_compression_hdr::qs_included

Definition at line 207 of file cram_structs.h.

int cram_block_compression_hdr::read_names_included

Definition at line 208 of file cram_structs.h.

struct cram_map* cram_block_compression_hdr::rec_encoding_map[CRAM_MAP_HASH]

Definition at line 221 of file cram_structs.h.

int32_t cram_block_compression_hdr::ref_seq_id

Definition at line 196 of file cram_structs.h.

int32_t cram_block_compression_hdr::ref_seq_span

Definition at line 198 of file cram_structs.h.

int32_t cram_block_compression_hdr::ref_seq_start

Definition at line 197 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::RG_codec

Definition at line 228 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::RI_codec

Definition at line 252 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::RL_codec

Definition at line 226 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::RN_codec

Definition at line 249 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::RS_codec

Definition at line 245 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::SC_codec

Definition at line 242 of file cram_structs.h.

char cram_block_compression_hdr::substitution_matrix[5][4]

Definition at line 211 of file cram_structs.h.

struct cram_map* cram_block_compression_hdr::tag_encoding_map[CRAM_MAP_HASH]

Definition at line 222 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::TC_codec

Definition at line 234 of file cram_structs.h.

cram_block* cram_block_compression_hdr::TD_blk

Definition at line 214 of file cram_structs.h.

string_alloc_t* cram_block_compression_hdr::TD_keys

Definition at line 218 of file cram_structs.h.

unsigned char** cram_block_compression_hdr::TL

Definition at line 216 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::TL_codec

Definition at line 236 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::TM_codec

Definition at line 253 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::TN_codec

Definition at line 235 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::TS_codec

Definition at line 232 of file cram_structs.h.

struct cram_codec* cram_block_compression_hdr::TV_codec

Definition at line 254 of file cram_structs.h.

char* cram_block_compression_hdr::uncomp

Definition at line 256 of file cram_structs.h.

size_t cram_block_compression_hdr::uncomp_alloc

Definition at line 257 of file cram_structs.h.

size_t cram_block_compression_hdr::uncomp_size

Definition at line 257 of file cram_structs.h.

int cram_block_compression_hdr::unmapped_placed

Definition at line 206 of file cram_structs.h.

int cram_block_compression_hdr::unmapped_qs_included

Definition at line 205 of file cram_structs.h.

The documentation for this struct was generated from the following file:

E:/git/nvbio/contrib/htslib/cram/cram_structs.h

Detailed description

Public Methods

Public Members

Member Function Documentation

Member Data Documentation