#include <stdint.h>
#include <cram/misc.h>

Macros
#define	ITF8_MACROS

Functions

int	cram_load_reference (cram_fd fd, char fn)

int	refs2id (refs_t r, SAM_hdr bfd)

void	refs_free (refs_t *r)

char *	cram_get_ref (cram_fd *fd, int id, int start, int end)

void	cram_ref_incr (refs_t *r, int id)

void	cram_ref_decr (refs_t *r, int id)


cram_container *	cram_new_container (int nrec, int nslice)

void	cram_free_container (cram_container *c)

cram_container *	cram_read_container (cram_fd *fd)

int	cram_write_container (cram_fd fd, cram_container h)

int	cram_flush_container (cram_fd fd, cram_container c)

int	cram_flush_container_mt (cram_fd fd, cram_container c)


cram_block_compression_hdr *	cram_new_compression_header (void)

void	cram_free_compression_header (cram_block_compression_hdr *hdr)


void	cram_free_slice_header (cram_block_slice_hdr *hdr)

void	cram_free_slice (cram_slice *s)

cram_slice *	cram_new_slice (enum cram_content_type type, int nrecs)

cram_slice *	cram_read_slice (cram_fd *fd)


cram_file_def *	cram_read_file_def (cram_fd *fd)

int	cram_write_file_def (cram_fd fd, cram_file_def def)

void	cram_free_file_def (cram_file_def *def)


SAM_hdr *	cram_read_SAM_hdr (cram_fd *fd)

int	cram_write_SAM_hdr (cram_fd fd, SAM_hdr hdr)


cram_fd *	cram_open (const char filename, const char mode)

cram_fd *	cram_dopen (cram_FILE fp, const char filename, const char *mode)

int	cram_close (cram_fd *fd)

int	cram_seek (cram_fd *fd, off_t offset, int whence)

int	cram_flush (cram_fd *fd)

int	cram_eof (cram_fd *fd)

int	cram_set_option (cram_fd *fd, enum cram_option opt,...)

int	cram_set_voption (cram_fd *fd, enum cram_option opt, va_list args)

int	cram_set_header (cram_fd fd, SAM_hdr hdr)

#define	CRAM_KEY(a, b) (((a)<<8)\|((b)))

#define	itf8_get(c, v) (((uc)(c)[0]<0x80)?((v)=(uc)(c)[0],1):(((uc)(c)[0]<0xc0)?((v)=(((uc)(c)[0]<<8)\|(uc)(c)[1])&0x3fff,2):(((uc)(c)[0]<0xe0)?((v)=(((uc)(c)[0]<<16)\|((uc)(c)[1]<<8)\|(uc)(c)[2])&0x1fffff,3):(((uc)(c)[0]<0xf0)?((v)=(((uc)(c)[0]<<24)\|((uc)(c)[1]<<16)\|((uc)(c)[2]<<8)\|(uc)(c)[3])&0x0fffffff,4):(*(v)=(((uc)(c)[0]&0x0f)<<28)\|((uc)(c)[1]<<20)\|((uc)(c)[2]<<12)\|((uc)(c)[3]<<4)\|((uc)(c)[4]&0x0f),5)))))

#define	itf8_put(c, v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)\|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)\|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)\|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0\|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))

#define	itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?4:5)

int	itf8_decode (cram_fd fd, int32_t val)

int	itf8_put_blk (cram_block *blk, int val)

#define	BLOCK_SIZE(b) ((b)->byte)

#define	BLOCK_DATA(b) ((b)->data)

#define	BLOCK_END(b) (&(b)->data[(b)->byte])

#define	BLOCK_RESIZE(b, l)

#define	BLOCK_GROW(b, l) BLOCK_RESIZE((b), BLOCK_SIZE((b)) + (l))

#define	BLOCK_APPEND(b, s, l)

#define	BLOCK_APPEND_CHAR(b, c)

#define	BLOCK_APPENDF_1(b, buf, fmt, a1)

#define	BLOCK_APPENDF_2(b, buf, fmt, a1, a2)

#define	BLOCK_UPLEN(b) (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b))

cram_block *	cram_new_block (enum cram_content_type content_type, int content_id)

cram_block *	cram_read_block (cram_fd *fd)

int	cram_write_block (cram_fd fd, cram_block b)

void	cram_free_block (cram_block *b)

char *	zlib_mem_inflate (char cdata, size_t csize, size_t size)

int	cram_uncompress_block (cram_block *b)

int	cram_compress_block (cram_fd fd, cram_block b, cram_metrics *metrics, int level, int strat, int level2, int strat2)

cram_metrics *	cram_new_metrics (void)

char *	cram_block_method2str (enum cram_block_method m)

char *	cram_content_type2str (enum cram_content_type t)

Detailed Description

Include cram.h instead.

This is an internal part of the CRAM system and is automatically included when you #include cram.h.

Implements the low level CRAM I/O primitives. This includes basic data types such as byte, int, ITF-8, maps, bitwise I/O, etc.

Definition in file cram_io.h.

Macro Definition Documentation

#define BLOCK_APPEND	(	b,
		s,
		l
	)

Value:

do {                              \
        BLOCK_GROW((b),(l));              \
        memcpy(BLOCK_END((b)), (s), (l)); \
        BLOCK_SIZE((b)) += (l);           \
    } while (0)

Definition at line 211 of file cram_io.h.

#define BLOCK_APPEND_CHAR	(	b,
		c
	)

Value:

do {                              \
        BLOCK_GROW((b),1);                \
        (b)->data[(b)->byte++] = (c);     \
    } while (0)

Definition at line 219 of file cram_io.h.

#define BLOCK_APPENDF_1	(	b,
		buf,
		fmt,
		a1
	)

Value:

do {                                            \
        int l = sprintf((buf), (fmt), (a1));            \
        BLOCK_APPEND((b), (buf), l);                    \
    } while (0)

Definition at line 226 of file cram_io.h.

#define BLOCK_APPENDF_2	(	b,
		buf,
		fmt,
		a1,
		a2
	)

Value:

do {                                            \
        int l = sprintf((buf), (fmt), (a1), (a2));      \
        BLOCK_APPEND((b), (buf), l);                    \
    } while (0)

Definition at line 233 of file cram_io.h.

#define BLOCK_DATA ( b) ((b)->data)

Definition at line 193 of file cram_io.h.

#define BLOCK_END ( b) (&(b)->data[(b)->byte])

Definition at line 196 of file cram_io.h.

#define BLOCK_GROW	(	b,
		l
	)	BLOCK_RESIZE((b), BLOCK_SIZE((b)) + (l))

Definition at line 208 of file cram_io.h.

#define BLOCK_RESIZE	(	b,
		l
	)

Value:

do {                                                    \
        while((b)->alloc <= (l)) {                              \
            (b)->alloc = (b)->alloc ? (b)->alloc*1.5 : 1024;    \
            (b)->data = realloc((b)->data, (b)->alloc);         \
        }                                                       \
     } while(0)

Definition at line 199 of file cram_io.h.

#define BLOCK_SIZE ( b) ((b)->byte)

Definition at line 192 of file cram_io.h.

#define BLOCK_UPLEN ( b) (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b))

Definition at line 239 of file cram_io.h.

#define CRAM_KEY	(	a,
		b
	)	(((a)<<8)\|((b)))

ITF8 encoding and decoding.

Also see the itf8_get and itf8_put macros.

INTERNAL: Converts two characters into an integer for use in switch{}

Definition at line 61 of file cram_io.h.

#define itf8_get	(	c,
		v
	)	(((uc)(c)[0]<0x80)?((v)=(uc)(c)[0],1):(((uc)(c)[0]<0xc0)?((v)=(((uc)(c)[0]<<8)\|(uc)(c)[1])&0x3fff,2):(((uc)(c)[0]<0xe0)?((v)=(((uc)(c)[0]<<16)\|((uc)(c)[1]<<8)\|(uc)(c)[2])&0x1fffff,3):(((uc)(c)[0]<0xf0)?((v)=(((uc)(c)[0]<<24)\|((uc)(c)[1]<<16)\|((uc)(c)[2]<<8)\|(uc)(c)[3])&0x0fffffff,4):(*(v)=(((uc)(c)[0]&0x0f)<<28)\|((uc)(c)[1]<<20)\|((uc)(c)[2]<<12)\|((uc)(c)[3]<<4)\|((uc)(c)[4]&0x0f),5)))))

Definition at line 95 of file cram_io.h.

#define ITF8_MACROS

Definition at line 49 of file cram_io.h.

#define itf8_put	(	c,
		v
	)	((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)\|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)\|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)\|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0\|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))

Definition at line 97 of file cram_io.h.

#define itf8_size ( v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?4:5)

Definition at line 99 of file cram_io.h.

Function Documentation

char* cram_block_method2str ( enum cram_block_method m)

Definition at line 969 of file cram_io.c.

int cram_close ( cram_fd * fd)

Closes a CRAM file.

Returns: Returns 0 on success; -1 on failure

Definition at line 3409 of file cram_io.c.

int cram_compress_block	(	cram_fd *	fd,
		cram_block *	b,
		cram_metrics *	metrics,
		int	level,
		int	strat,
		int	level2,
		int	strat2
	)

Compresses a block.

Compresses a block using one of two different zlib strategies. If we only want one choice set strat2 to be -1.

The logic here is that sometimes Z_RLE does a better job than Z_FILTERED or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is significantly faster.

Returns: Returns 0 on success; -1 on failure

Definition at line 866 of file cram_io.c.

char* cram_content_type2str ( enum cram_content_type t)

Definition at line 979 of file cram_io.c.

cram_fd* cram_dopen	(	cram_FILE *	fp,
		const char *	filename,
		const char *	mode
	)

Opens an existing stream for reading or writing.

Returns: Returns file handle on success; NULL on failure.

cram_FILE is either htslib's hFILE or stdio's FILE, depending on how cram_structs.h has been configured.

Definition at line 3253 of file cram_io.c.

int cram_eof ( cram_fd * fd)

Checks for end of file on a cram_fd stream.

Returns: Returns 0 if not at end of file 1 if we hit an expected EOF (end of range or EOF block) 2 for other EOF (end of stream without EOF block)

Definition at line 3502 of file cram_io.c.

int cram_flush ( cram_fd * fd)

Definition at line 3390 of file cram_io.c.

int cram_flush_container	(	cram_fd *	fd,
		cram_container *	c
	)

Flushes a container to disk.

Flushes a completely or partially full container to disk, writing container structure, header and blocks. This also calls the encoder functions.

Returns: Returns 0 on success; -1 on failure

Definition at line 2311 of file cram_io.c.

int cram_flush_container_mt	(	cram_fd *	fd,
		cram_container *	c
	)

Definition at line 2374 of file cram_io.c.

void cram_free_block ( cram_block * b)

Frees a CRAM block, deallocating internal data too.

Definition at line 755 of file cram_io.c.

void cram_free_compression_header ( cram_block_compression_hdr * hdr)

Frees a cram_block_compression_hdr

Definition at line 2426 of file cram_io.c.

void cram_free_container ( cram_container * c)

Definition at line 2070 of file cram_io.c.

void cram_free_file_def ( cram_file_def * def)

Frees a cram_file_def structure.

Definition at line 2786 of file cram_io.c.

void cram_free_slice ( cram_slice * s)

Frees a slice

Definition at line 2514 of file cram_io.c.

void cram_free_slice_header ( cram_block_slice_hdr * hdr)

Slices and slice headers

Frees a slice header

Definition at line 2502 of file cram_io.c.

char* cram_get_ref	(	cram_fd *	fd,
		int	id,
		int	start,
		int	end
	)

Returns a portion of a reference sequence from start to end inclusive.

The returned pointer is owned by the cram_file fd and should not be freed by the caller. It is valid only until the next cram_get_ref is called with the same fd parameter (so is thread-safe if given multiple files).

To return the entire reference sequence, specify start as 1 and end as 0.

Returns: Returns reference on success; NULL on failure

Definition at line 1770 of file cram_io.c.

int cram_load_reference	(	cram_fd *	fd,
		char *	fn
	)

Reference sequence handling

Loads a reference set from fn and stores in the cram_fd.

Returns: Returns 0 on success; -1 on failure

Definition at line 1963 of file cram_io.c.

cram_block* cram_new_block	(	enum cram_content_type	content_type,
		int	content_id
	)

CRAM blocks - the dynamically growable data block. We have code to create, update, (un)compress and read/write.

These are derived from the deflate_interlaced.c blocks, but with the CRAM extension of content types and IDs.

Allocates a new cram_block structure with a specified content_type and id.

Returns: Returns block pointer on success; NULL on failure

Definition at line 662 of file cram_io.c.

cram_block_compression_hdr* cram_new_compression_header ( void )

Compression headers; the first part of the container

Creates a new blank container compression header

Returns: Returns header ptr on success; NULL on failure

Definition at line 2400 of file cram_io.c.

cram_container* cram_new_container	(	int	nrec,
		int	nslice
	)

Containers

Creates a new container, specifying the maximum number of slices and records permitted.

Returns: Returns cram_container ptr on success; NULL on failure

Definition at line 1995 of file cram_io.c.

cram_metrics* cram_new_metrics ( void )

Definition at line 959 of file cram_io.c.

cram_slice* cram_new_slice	(	enum cram_content_type	type,
		int	nrecs
	)

Creates a new empty slice in memory, for subsequent writing to disk.

Returns: Returns cram_slice ptr on success; NULL on failure

Definition at line 2591 of file cram_io.c.

cram_fd* cram_open	(	const char *	filename,
		const char *	mode
	)

The top-level cram opening, closing and option handling

Opens a CRAM file for read (mode "rb") or write ("wb").

The filename may be "-" to indicate stdin or stdout.

Returns: Returns file handle on success; NULL on failure.

Definition at line 3217 of file cram_io.c.

cram_block* cram_read_block ( cram_fd * fd)

Reads a block from a cram file.

Returns: Returns cram_block pointer on success; NULL on failure

Definition at line 685 of file cram_io.c.

cram_container* cram_read_container ( cram_fd * fd)

Reads a container header.

Returns: Returns cram_container on success; NULL on failure or no container left (fd->err == 0).

Definition at line 2137 of file cram_io.c.

cram_file_def* cram_read_file_def ( cram_fd * fd)

CRAM file definition (header)

Reads a CRAM file definition structure.

Returns: Returns file_def ptr on success; NULL on failure

Definition at line 2748 of file cram_io.c.

SAM_hdr* cram_read_SAM_hdr ( cram_fd * fd)

SAM header I/O

Reads the SAM header from the first CRAM data block.

Also performs minimal parsing to extract read-group and sample information.

Returns: Returns SAM hdr ptr on success; NULL on failure

Definition at line 2803 of file cram_io.c.

cram_slice* cram_read_slice ( cram_fd * fd)

Loads an entire slice.

FIXME: In 1.0 the native unit of slices within CRAM is broken as slices contain references to objects in other slices. To work around this while keeping the slice oriented outer loop we read all slices and stitch them together into a fake large slice instead.

Returns: Returns cram_slice ptr on success; NULL on failure

Definition at line 2656 of file cram_io.c.

void cram_ref_decr	(	refs_t *	r,
		int	id
	)

Definition at line 1600 of file cram_io.c.

void cram_ref_incr	(	refs_t *	r,
		int	id
	)

Definition at line 1568 of file cram_io.c.

int cram_seek	(	cram_fd *	fd,
		off_t	offset,
		int	whence
	)

Definition at line 3363 of file cram_io.c.

int cram_set_header	(	cram_fd *	fd,
		SAM_hdr *	hdr
	)

Attaches a header to a cram_fd.

This should be used when creating a new cram_fd for writing where we have an SAM_hdr already constructed (eg from a file we've read in).

Returns: Returns 0 on success; -1 on failure

Definition at line 1341 of file cram_io.c.

int cram_set_option	(	cram_fd *	fd,
		enum cram_option	opt,
			...
	)

Sets options on the cram_fd.

See CRAM_OPT_* definitions in cram_structs.h. Use this immediately after opening.

Returns: Returns 0 on success; -1 on failure

Definition at line 3514 of file cram_io.c.

int cram_set_voption	(	cram_fd *	fd,
		enum cram_option	opt,
		va_list	args
	)

Sets options on the cram_fd.

See CRAM_OPT_* definitions in cram_structs.h. Use this immediately after opening.

Returns: Returns 0 on success; -1 on failure

Definition at line 3532 of file cram_io.c.

int cram_uncompress_block ( cram_block * b)

Uncompresses a CRAM block, if compressed.

Returns: Returns 0 on success; -1 on failure

Definition at line 766 of file cram_io.c.

int cram_write_block	(	cram_fd *	fd,
		cram_block *	b
	)

Writes a CRAM block.

Returns: Returns 0 on success; -1 on failure

Definition at line 732 of file cram_io.c.

int cram_write_container	(	cram_fd *	fd,
		cram_container *	h
	)

Writes a container structure.

Returns: Returns 0 on success; -1 on failure

Definition at line 2229 of file cram_io.c.

int cram_write_file_def	(	cram_fd *	fd,
		cram_file_def *	def
	)

Writes a cram_file_def structure to cram_fd.

Returns: Returns 0 on success; -1 on failure

Definition at line 2782 of file cram_io.c.

int cram_write_SAM_hdr	(	cram_fd *	fd,
		SAM_hdr *	hdr
	)

Writes a CRAM SAM header.

Returns: Returns 0 on success; -1 on failure

Definition at line 2936 of file cram_io.c.

int itf8_decode	(	cram_fd *	fd,
		int32_t *	val
	)

Reads an integer in ITF-8 encoding from 'fd' and stores it in *val.

Returns: Returns the number of bytes read on success; -1 on failure

Definition at line 108 of file cram_io.c.

int itf8_put_blk	(	cram_block *	blk,
		int	val
	)

Pushes a value in ITF8 format onto the end of a block.

This shouldn't be used for high-volume data as it is not the fastest method.

Returns: Returns the number of bytes written

Definition at line 461 of file cram_io.c.

int refs2id	(	refs_t *	r,
		SAM_hdr *	bfd
	)

Generates a lookup table in refs based on the SQ headers in SAM_hdr.

Indexes references by the order they appear in a BAM file. This may not necessarily be the same order they appear in the fasta reference file.

Returns: Returns 0 on success; -1 on failure

Definition at line 1248 of file cram_io.c.

void refs_free ( refs_t * r)

Definition at line 1038 of file cram_io.c.

char* zlib_mem_inflate	(	char *	cdata,
		size_t	csize,
		size_t *	size
	)

Uncompress a memory block using Zlib.

Returns: Returns 0 on success; -1 on failure

Definition at line 530 of file cram_io.c.

Macros

Functions

Detailed Description

Macro Definition Documentation

Function Documentation