cram_encode.c File Reference

#include <stdio.h>
#include <errno.h>
#include <assert.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <math.h>
#include <ctype.h>
#include "cram/cram.h"
#include "cram/os.h"
#include "cram/md5.h"

Macros
#define	Z_CRAM_STRAT   Z_FILTERED
#define	TAG_ID(a)   ((#a[0]<<8)+#a[1])

Functions
cram_block *	cram_encode_compression_header (cram_fd *fd, cram_container *c, cram_block_compression_hdr *h)
cram_block *	cram_encode_slice_header (cram_fd *fd, cram_slice *s)
int	cram_encode_container (cram_fd *fd, cram_container *c)
int	cram_put_bam_seq (cram_fd *fd, bam_seq_t *b)

Macro Definition Documentation

#define TAG_ID

(

a

)

((#a[0]<<8)+#a[1])

#define Z_CRAM_STRAT   Z_FILTERED

Function Documentation

cram_block* cram_encode_compression_header	(	cram_fd *	fd,
		cram_container *	c,
		cram_block_compression_hdr *	h
	)

INTERNAL: Encodes a compression header block into a generic cram_block structure.

Returns

Returns cram_block ptr on success; NULL on failure

int cram_encode_container	(	cram_fd *	fd,
		cram_container *	c
	)

INTERNAL: Encodes all slices in a container into blocks.

Returns

Returns 0 on success; -1 on failure

FIXME: separate into encode_container and write_container. Ideally we should be able to do read_container / write_container or decode_container / encode_container.

cram_block* cram_encode_slice_header	(	cram_fd *	fd,
		cram_slice *	s
	)

INTERNAL: Encodes a slice compression header.

Returns

Returns cram_block on success; NULL on failure

int cram_put_bam_seq	(	cram_fd *	fd,
		bam_seq_t *	b
	)

Write iterator: put BAM format sequences into a CRAM file.

We buffer up a containers worth of data at a time.

FIXME: break this into smaller pieces.

Returns

Returns 0 on success; -1 on failure