cram_encode.h File Reference

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Functions
int	cram_put_bam_seq (cram_fd *fd, bam_seq_t *b)
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)

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 encoding portion of CRAM I/O. Also see cram_codecs.[ch] for the actual encoding functions themselves.

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