cram_decode.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"

Classes
struct	cram_decode_job

Functions
int	cram_decode_TD (char *cp, cram_block_compression_hdr *h)
cram_block_compression_hdr *	cram_decode_compression_header (cram_fd *fd, cram_block *b)
int	cram_dependent_data_series (cram_fd *fd, cram_block_compression_hdr *hdr, cram_slice *s)
cram_block_slice_hdr *	cram_decode_slice_header (cram_fd *fd, cram_block *b)
int	cram_decode_slice (cram_fd *fd, cram_container *c, cram_slice *s, SAM_hdr *bfd)
void *	cram_decode_slice_thread (void *arg)
int	cram_decode_slice_mt (cram_fd *fd, cram_container *c, cram_slice *s, SAM_hdr *bfd)
cram_record *	cram_get_seq (cram_fd *fd)
int	cram_get_bam_seq (cram_fd *fd, bam_seq_t **bam)

Function Documentation

cram_block_compression_hdr* cram_decode_compression_header	(	cram_fd *	fd,
		cram_block *	b
	)

INTERNAL: Decodes a CRAM block compression header.

Returns

Returns header ptr on success; NULL on failure

int cram_decode_slice	(	cram_fd *	fd,
		cram_container *	c,
		cram_slice *	s,
		SAM_hdr *	hdr
	)

INTERNAL: Decode an entire slice from container blocks. Fills out s->crecs[] array.

Returns

Returns 0 on success; -1 on failure

cram_block_slice_hdr* cram_decode_slice_header	(	cram_fd *	fd,
		cram_block *	b
	)

INTERNAL: Decodes a CRAM (un)mapped slice header block.

Returns

Returns slice header ptr on success; NULL on failure

int cram_decode_slice_mt	(	cram_fd *	fd,
		cram_container *	c,
		cram_slice *	s,
		SAM_hdr *	bfd
	)

void* cram_decode_slice_thread

(

void *

arg

)

int cram_decode_TD	(	char *	cp,
		cram_block_compression_hdr *	h
	)

int cram_dependent_data_series	(	cram_fd *	fd,
		cram_block_compression_hdr *	hdr,
		cram_slice *	s
	)

int cram_get_bam_seq	(	cram_fd *	fd,
		bam_seq_t **	bam
	)

Read the next cram record and convert it to a bam_seq_t struct.

Returns

Returns 0 on success; -1 on EOF or failure (check fd->err)

cram_record* cram_get_seq

(

cram_fd *

fd

)

Read the next cram record and return it as a cram_record.

Note that to decode cram_record the caller will need to look up some data in the current slice, pointed to by fd->ctr->slice. This is valid until the next call to cram_get_seq (which may invalidate it).

Returns

Returns record pointer on success (do not free); NULL on failure