cram_structs.h File Reference

#include <stdint.h>
#include "cram/thread_pool.h"
#include "cram/bam.h"

Go to the source code of this file.

Classes
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	TN_external
#define	TS_external
#define	MAX_STAT_VAL   1024
#define	CRAM_1_VERS   100
#define	CRAM_2_VERS   200
#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_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	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)
#define	CRAM_EXT_IN   0
#define	CRAM_EXT_QUAL   1
#define	CRAM_EXT_NAME   2
#define	CRAM_EXT_TS_NP   3
#define	CRAM_EXT_TAG   4
#define	CRAM_EXT_TAG_S   "\004"
#define	CRAM_EXT_BA   5
#define	CRAM_EXT_TN   6
#define	CRAM_EXT_SC   7
#define	CRAM_EXT_REF   8

Typedefs
typedef FILE	cram_FILE
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_block_method { BM_ERROR = -1, RAW = 0, GZIP = 1, BZIP2 = 2 }
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_option {   CRAM_OPT_DECODE_MD, CRAM_OPT_PREFIX, CRAM_OPT_VERBOSITY, CRAM_OPT_SEQS_PER_SLICE,   CRAM_OPT_SLICES_PER_CONTAINER, CRAM_OPT_RANGE, CRAM_OPT_VERSION, CRAM_OPT_EMBED_REF,   CRAM_OPT_IGNORE_MD5, CRAM_OPT_REFERENCE, CRAM_OPT_MULTI_SEQ_PER_SLICE, CRAM_OPT_NO_REF,   CRAM_OPT_USE_BZIP2, CRAM_OPT_SHARED_REF, CRAM_OPT_NTHREADS, CRAM_OPT_THREAD_POOL }

Macro Definition Documentation

#define CRAM_1_VERS   100

Definition at line 142 of file cram_structs.h.

#define CRAM_2_VERS   200

Definition at line 143 of file cram_structs.h.

#define cram_aux

(

c)

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

Definition at line 416 of file cram_structs.h.

#define cram_cigar

(

c)

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

Definition at line 421 of file cram_structs.h.

#define CRAM_EXT_BA   5

Definition at line 743 of file cram_structs.h.

#define CRAM_EXT_IN   0

Definition at line 737 of file cram_structs.h.

#define CRAM_EXT_NAME   2

Definition at line 739 of file cram_structs.h.

#define CRAM_EXT_QUAL   1

Definition at line 738 of file cram_structs.h.

#define CRAM_EXT_REF   8

Definition at line 746 of file cram_structs.h.

#define CRAM_EXT_SC   7

Definition at line 745 of file cram_structs.h.

#define CRAM_EXT_TAG   4

Definition at line 741 of file cram_structs.h.

#define CRAM_EXT_TAG_S   "\004"

Definition at line 742 of file cram_structs.h.

#define CRAM_EXT_TN   6

Definition at line 744 of file cram_structs.h.

#define CRAM_EXT_TS_NP   3

Definition at line 740 of file cram_structs.h.

#define CRAM_FDUP   1

Definition at line 725 of file cram_structs.h.

#define CRAM_FLAG_DETACHED   (1<<1)

Definition at line 733 of file cram_structs.h.

#define CRAM_FLAG_MATE_DOWNSTREAM   (1<<2)

Definition at line 734 of file cram_structs.h.

#define CRAM_FLAG_PRESERVE_QUAL_SCORES   (1<<0)

Definition at line 732 of file cram_structs.h.

#define CRAM_FPAIRED   256

Definition at line 717 of file cram_structs.h.

#define CRAM_FPROPER_PAIR   128

Definition at line 718 of file cram_structs.h.

#define CRAM_FQCFAIL   2

Definition at line 724 of file cram_structs.h.

#define CRAM_FREAD1   16

Definition at line 721 of file cram_structs.h.

#define CRAM_FREAD2   8

Definition at line 722 of file cram_structs.h.

#define CRAM_FREVERSE   32

Definition at line 720 of file cram_structs.h.

#define CRAM_FSECONDARY   4

Definition at line 723 of file cram_structs.h.

#define CRAM_FUNMAP   64

Definition at line 719 of file cram_structs.h.

#define CRAM_M_REVERSE   1

Definition at line 727 of file cram_structs.h.

#define CRAM_M_UNMAP   2

Definition at line 728 of file cram_structs.h.

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

Definition at line 192 of file cram_structs.h.

#define CRAM_MAP_HASH   32

Definition at line 191 of file cram_structs.h.

#define cram_mstrand

(

c)

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

Definition at line 420 of file cram_structs.h.

#define cram_name_len

(

c)

((c)->name_len)

Definition at line 418 of file cram_structs.h.

#define cram_qname

(

c)

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

Definition at line 413 of file cram_structs.h.

#define cram_qual

(

c)

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

Definition at line 415 of file cram_structs.h.

#define cram_seq

(

c)

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

Definition at line 414 of file cram_structs.h.

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

Definition at line 417 of file cram_structs.h.

#define cram_strand

(

c)

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

Definition at line 419 of file cram_structs.h.

#define CRAM_SUBST_MATRIX   "CGTNAGTNACTNACGNACGT"

Definition at line 96 of file cram_structs.h.

#define MAX_STAT_VAL   1024

Definition at line 103 of file cram_structs.h.

#define SEQS_PER_SLICE   10000

Definition at line 93 of file cram_structs.h.

#define SLICE_PER_CNT   1

Definition at line 94 of file cram_structs.h.

#define TN_external

Definition at line 98 of file cram_structs.h.

#define TS_external

Definition at line 100 of file cram_structs.h.

Typedef Documentation

typedef struct cram_fd cram_fd

typedef FILE cram_FILE

Definition at line 90 of file cram_structs.h.

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

Enumeration Type Documentation

enum cram_block_method

Enumerator
BM_ERROR
RAW
GZIP
BZIP2

Definition at line 147 of file cram_structs.h.

enum cram_content_type

Enumerator
CT_ERROR
FILE_HEADER
COMPRESSION_HEADER
MAPPED_SLICE
UNMAPPED_SLICE
EXTERNAL
CORE

Definition at line 154 of file cram_structs.h.

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

Definition at line 113 of file cram_structs.h.

enum cram_external_type

Enumerator
E_INT
E_LONG
E_BYTE
E_BYTE_ARRAY
E_BYTE_ARRAY_BLOCK

Definition at line 126 of file cram_structs.h.

enum cram_option

Enumerator
CRAM_OPT_DECODE_MD
CRAM_OPT_PREFIX
CRAM_OPT_VERBOSITY
CRAM_OPT_SEQS_PER_SLICE
CRAM_OPT_SLICES_PER_CONTAINER
CRAM_OPT_RANGE
CRAM_OPT_VERSION
CRAM_OPT_EMBED_REF
CRAM_OPT_IGNORE_MD5
CRAM_OPT_REFERENCE
CRAM_OPT_MULTI_SEQ_PER_SLICE
CRAM_OPT_NO_REF
CRAM_OPT_USE_BZIP2
CRAM_OPT_SHARED_REF
CRAM_OPT_NTHREADS
CRAM_OPT_THREAD_POOL

Definition at line 696 of file cram_structs.h.