cram_decode.h File Reference

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Functions
cram_record *	cram_get_seq (cram_fd *fd)
int	cram_get_bam_seq (cram_fd *fd, bam_seq_t **bam)
cram_block_compression_hdr *	cram_decode_compression_header (cram_fd *fd, cram_block *b)
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 *hdr)

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

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_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