cram_structs.h File Reference

#include <stdint.h>
#include "cram/thread_pool.h"
#include "cram/string_alloc.h"
#include "htslib/khash.h"

Go to the source code of this file.

Classes
union	pmap_t
struct	cram_stats
struct	cram_file_def
struct	cram_metrics
struct	cram_block
struct	cram_block_compression_hdr
struct	cram_map
struct	cram_block_slice_hdr
struct	cram_container
struct	cram_record
struct	cram_feature
struct	cram_slice
struct	ref_entry
struct	refs_t
struct	cram_index
struct	cram_range
struct	spare_bams
struct	cram_fd

Macros
#define	SEQS_PER_SLICE   10000
#define	SLICE_PER_CNT   1
#define	CRAM_SUBST_MATRIX   "CGTNAGTNACTNACGNACGT"
#define	MAX_STAT_VAL   1024
#define	CRAM_MAJOR_VERS(v)   ((v) >> 8)
#define	CRAM_MINOR_VERS(v)   ((v) & 0xff)
#define	CRAM_MAP_HASH   32
#define	CRAM_MAP(a, b)   (((a)*3+(b))&(CRAM_MAP_HASH-1))
#define	cram_qname(c)   (&(c)->s->name_blk->data[(c)->name])
#define	cram_seq(c)   (&(c)->s->seqs_blk->data[(c)->seq])
#define	cram_qual(c)   (&(c)->s->qual_blk->data[(c)->qual])
#define	cram_aux(c)   (&(c)->s->aux_blk->data[(c)->aux])
#define	cram_seqi(c, i)   (cram_seq((c))[(i)])
#define	cram_name_len(c)   ((c)->name_len)
#define	cram_strand(c)   (((c)->flags & BAM_FREVERSE) != 0)
#define	cram_mstrand(c)   (((c)->flags & BAM_FMREVERSE) != 0)
#define	cram_cigar(c)   (&((cr)->s->cigar)[(c)->cigar])
#define	CRAM_CIGAR
#define	CRAM_SEQ
#define	CRAM_FPAIRED   256
#define	CRAM_FPROPER_PAIR   128
#define	CRAM_FUNMAP   64
#define	CRAM_FREVERSE   32
#define	CRAM_FREAD1   16
#define	CRAM_FREAD2   8
#define	CRAM_FSECONDARY   4
#define	CRAM_FQCFAIL   2
#define	CRAM_FDUP   1
#define	DS_aux_S   "\001"
#define	DS_aux_OQ_S   "\002"
#define	DS_aux_BQ_S   "\003"
#define	DS_aux_BD_S   "\004"
#define	DS_aux_BI_S   "\005"
#define	DS_aux_FZ_S   "\006"
#define	DS_aux_oq_S   "\007"
#define	DS_aux_os_S   "\010"
#define	DS_aux_oz_S   "\011"
#define	CRAM_M_REVERSE   1
#define	CRAM_M_UNMAP   2
#define	CRAM_FLAG_PRESERVE_QUAL_SCORES   (1<<0)
#define	CRAM_FLAG_DETACHED   (1<<1)
#define	CRAM_FLAG_MATE_DOWNSTREAM   (1<<2)

Typedefs
typedef unsigned char	uc
typedef struct cram_map	cram_map
typedef struct cram_slice	cram_slice
typedef struct ref_entry	ref_entry
typedef struct cram_index	cram_index
typedef struct spare_bams	spare_bams
typedef struct cram_fd	cram_fd

Enumerations
enum	cram_encoding {   E_NULL = 0, E_EXTERNAL = 1, E_GOLOMB = 2, E_HUFFMAN = 3,   E_BYTE_ARRAY_LEN = 4, E_BYTE_ARRAY_STOP = 5, E_BETA = 6, E_SUBEXP = 7,   E_GOLOMB_RICE = 8, E_GAMMA = 9 }
enum	cram_external_type {   E_INT = 1, E_LONG = 2, E_BYTE = 3, E_BYTE_ARRAY = 4,   E_BYTE_ARRAY_BLOCK = 5 }
enum	cram_DS_ID {   DS_CORE = 0, DS_aux = 1, DS_aux_OQ = 2, DS_aux_BQ = 3,   DS_aux_BD = 4, DS_aux_BI = 5, DS_aux_FZ = 6, DS_aux_oq = 7,   DS_aux_os = 8, DS_aux_oz = 9, DS_ref, DS_RN,   DS_QS, DS_IN, DS_SC, DS_BF,   DS_CF, DS_AP, DS_RG, DS_MQ,   DS_NS, DS_MF, DS_TS, DS_NP,   DS_NF, DS_RL, DS_FN, DS_FC,   DS_FP, DS_DL, DS_BA, DS_BS,   DS_TL, DS_RI, DS_RS, DS_PD,   DS_HC, DS_BB, DS_QQ, DS_TN,   DS_RN_len, DS_SC_len, DS_BB_len, DS_QQ_len,   DS_TC, DS_TM, DS_TV, DS_END }
enum	cram_block_method {   ERROR = -1, RAW = 0, GZIP = 1, BZIP2 = 2,   LZMA = 3, RANS = 4, RANS0 = 4, RANS1 = 10,   GZIP_RLE = 11 }
enum	cram_content_type {   CT_ERROR = -1, FILE_HEADER = 0, COMPRESSION_HEADER = 1, MAPPED_SLICE = 2,   UNMAPPED_SLICE = 3, EXTERNAL = 4, CORE = 5 }
enum	cram_fields {   CRAM_BF = 0x00000001, CRAM_AP = 0x00000002, CRAM_FP = 0x00000004, CRAM_RL = 0x00000008,   CRAM_DL = 0x00000010, CRAM_NF = 0x00000020, CRAM_BA = 0x00000040, CRAM_QS = 0x00000080,   CRAM_FC = 0x00000100, CRAM_FN = 0x00000200, CRAM_BS = 0x00000400, CRAM_IN = 0x00000800,   CRAM_RG = 0x00001000, CRAM_MQ = 0x00002000, CRAM_TL = 0x00004000, CRAM_RN = 0x00008000,   CRAM_NS = 0x00010000, CRAM_NP = 0x00020000, CRAM_TS = 0x00040000, CRAM_MF = 0x00080000,   CRAM_CF = 0x00100000, CRAM_RI = 0x00200000, CRAM_RS = 0x00400000, CRAM_PD = 0x00800000,   CRAM_HC = 0x01000000, CRAM_SC = 0x02000000, CRAM_BB = 0x04000000, CRAM_BB_len = 0x08000000,   CRAM_QQ = 0x10000000, CRAM_QQ_len = 0x20000000, CRAM_aux = 0x40000000, CRAM_ALL = 0x7fffffff }

Macro Definition Documentation

#define cram_aux

(

c

)

(&(c)->s->aux_blk->data[(c)->aux])

#define cram_cigar

(

c

)

(&((cr)->s->cigar)[(c)->cigar])

#define CRAM_CIGAR

Value:

(CRAM_FN | CRAM_FP | CRAM_FC | CRAM_DL | CRAM_IN | \
		    CRAM_SC | CRAM_HC | CRAM_PD | CRAM_RS | CRAM_RL | CRAM_BF)

#define CRAM_FDUP   1

#define CRAM_FLAG_DETACHED   (1<<1)

#define CRAM_FLAG_MATE_DOWNSTREAM   (1<<2)

#define CRAM_FLAG_PRESERVE_QUAL_SCORES   (1<<0)

#define CRAM_FPAIRED   256

#define CRAM_FPROPER_PAIR   128

#define CRAM_FQCFAIL   2

#define CRAM_FREAD1   16

#define CRAM_FREAD2   8

#define CRAM_FREVERSE   32

#define CRAM_FSECONDARY   4

#define CRAM_FUNMAP   64

#define CRAM_M_REVERSE   1

#define CRAM_M_UNMAP   2

#define CRAM_MAJOR_VERS

(

v

)

((v) >> 8)

#define CRAM_MAP	(		a,
			b
	)		(((a)*3+(b))&(CRAM_MAP_HASH-1))

#define CRAM_MAP_HASH   32

#define CRAM_MINOR_VERS

(

v

)

((v) & 0xff)

#define cram_mstrand

(

c

)

(((c)->flags & BAM_FMREVERSE) != 0)

#define cram_name_len

(

c

)

((c)->name_len)

#define cram_qname

(

c

)

(&(c)->s->name_blk->data[(c)->name])

#define cram_qual

(

c

)

(&(c)->s->qual_blk->data[(c)->qual])

#define cram_seq

(

c

)

(&(c)->s->seqs_blk->data[(c)->seq])

#define CRAM_SEQ

Value:

(CRAM_CIGAR | CRAM_BA | CRAM_QS | CRAM_BS | \
		  CRAM_RL    | CRAM_AP | CRAM_BB | CRAM_QQ)

#define cram_seqi	(		c,
			i
	)		(cram_seq((c))[(i)])

#define cram_strand

(

c

)

(((c)->flags & BAM_FREVERSE) != 0)

#define CRAM_SUBST_MATRIX   "CGTNAGTNACTNACGNACGT"

#define DS_aux_BD_S   "\004"

#define DS_aux_BI_S   "\005"

#define DS_aux_BQ_S   "\003"

#define DS_aux_FZ_S   "\006"

#define DS_aux_OQ_S   "\002"

#define DS_aux_oq_S   "\007"

#define DS_aux_os_S   "\010"

#define DS_aux_oz_S   "\011"

#define DS_aux_S   "\001"

#define MAX_STAT_VAL   1024

#define SEQS_PER_SLICE   10000

#define SLICE_PER_CNT   1

Typedef Documentation

typedef struct cram_fd cram_fd

typedef struct cram_index cram_index

typedef struct cram_map cram_map

typedef struct cram_slice cram_slice

typedef struct ref_entry ref_entry

typedef struct spare_bams spare_bams

typedef unsigned char uc

Enumeration Type Documentation

enum cram_block_method

Enumerator
ERROR
RAW
GZIP
BZIP2
LZMA
RANS
RANS0
RANS1
GZIP_RLE

enum cram_content_type

Enumerator
CT_ERROR
FILE_HEADER
COMPRESSION_HEADER
MAPPED_SLICE
UNMAPPED_SLICE
EXTERNAL
CORE

enum cram_DS_ID

Enumerator
DS_CORE
DS_aux
DS_aux_OQ
DS_aux_BQ
DS_aux_BD
DS_aux_BI
DS_aux_FZ
DS_aux_oq
DS_aux_os
DS_aux_oz
DS_ref
DS_RN
DS_QS
DS_IN
DS_SC
DS_BF
DS_CF
DS_AP
DS_RG
DS_MQ
DS_NS
DS_MF
DS_TS
DS_NP
DS_NF
DS_RL
DS_FN
DS_FC
DS_FP
DS_DL
DS_BA
DS_BS
DS_TL
DS_RI
DS_RS
DS_PD
DS_HC
DS_BB
DS_QQ
DS_TN
DS_RN_len
DS_SC_len
DS_BB_len
DS_QQ_len
DS_TC
DS_TM
DS_TV
DS_END

enum cram_encoding

Enumerator
E_NULL
E_EXTERNAL
E_GOLOMB
E_HUFFMAN
E_BYTE_ARRAY_LEN
E_BYTE_ARRAY_STOP
E_BETA
E_SUBEXP
E_GOLOMB_RICE
E_GAMMA

enum cram_external_type

Enumerator
E_INT
E_LONG
E_BYTE
E_BYTE_ARRAY
E_BYTE_ARRAY_BLOCK

enum cram_fields

Enumerator
CRAM_BF
CRAM_AP
CRAM_FP
CRAM_RL
CRAM_DL
CRAM_NF
CRAM_BA
CRAM_QS
CRAM_FC
CRAM_FN
CRAM_BS
CRAM_IN
CRAM_RG
CRAM_MQ
CRAM_TL
CRAM_RN
CRAM_NS
CRAM_NP
CRAM_TS
CRAM_MF
CRAM_CF
CRAM_RI
CRAM_RS
CRAM_PD
CRAM_HC
CRAM_SC
CRAM_BB
CRAM_BB_len
CRAM_QQ
CRAM_QQ_len
CRAM_aux
CRAM_ALL