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cram_decode.h File Reference

Go to the source code of this file.

Functions

cram_recordcram_get_seq (cram_fd *fd)
 
int cram_get_bam_seq (cram_fd *fd, bam_seq_t **bam)
 
cram_block_compression_hdrcram_decode_compression_header (cram_fd *fd, cram_block *b)
 
cram_block_slice_hdrcram_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.

Definition in file cram_decode.h.

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

Definition at line 125 of file cram_decode.c.

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

Definition at line 1335 of file cram_decode.c.

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

Definition at line 613 of file cram_decode.c.

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)

Definition at line 2126 of file cram_decode.c.

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

Definition at line 2073 of file cram_decode.c.