/usr/include/io_lib/sff.h is in libstaden-read-dev 1.14.6-2.
This file is owned by root:root, with mode 0o644.
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* Copyright (c) 2005, 2007 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
*
* 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
* Institute nor the names of its contributors may be used to endorse
* or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
* LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#ifndef _SFF_H_
#define _SFF_H_
#include "io_lib/Read.h"
#include "io_lib/os.h"
#include "io_lib/mFILE.h"
#ifdef __cplusplus
extern "C" {
#endif
/*
* This mirrors the order that the SFF header has on disc. We have one of
* these only.
*
* The flow and key are variable length fields as defined by flow_len
* and key_len.
* The on-disc structure is then also padded out with zeros to the 8-byte
* word boundary.
*/
typedef struct {
uint32_t magic;
char version[4];
uint64_t index_offset;
uint32_t index_len;
uint32_t nreads;
uint16_t header_len;
uint16_t key_len;
uint16_t flow_len;
uint8_t flowgram_format;
char *flow;
char *key;
} sff_common_header;
#define SFF_MAGIC 0x2e736666 /* ".sff" */
#define SFF_VERSION "\0\0\0\1"
/*
* We have one read_header per "reading" in the SFF archive.
* It too is padded to an 8-byte boundary.
*/
typedef struct {
uint16_t header_len;
uint16_t name_len;
uint32_t nbases;
uint16_t clip_qual_left;
uint16_t clip_qual_right;
uint16_t clip_adapter_left;
uint16_t clip_adapter_right;
char *name;
} sff_read_header;
/*
* We have one read_data section per reading, following the read_header.
* It is padded to an 8-byte boundary.
*/
typedef struct {
uint16_t *flowgram; /* x 100.0 */
uint8_t *flow_index; /* relative to last */
char *bases;
uint8_t *quality;
} sff_read_data;
/*
* Low level functions to decode SFF internals
*/
sff_common_header *decode_sff_common_header(unsigned char *buf);
sff_common_header *read_sff_common_header(mFILE *mf);
void free_sff_common_header(sff_common_header *h);
sff_read_header *decode_sff_read_header(unsigned char *buf);
void free_sff_read_header(sff_read_header *h);
sff_read_header *read_sff_read_header(mFILE *mf);
void free_sff_read_data(sff_read_data *d);
sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases);
/*
* Loads the first SFF sequence from an SFF container and returns as a Read.
*/
Read *mfread_sff(mFILE *mf);
#ifdef __cplusplus
}
#endif
#endif /* _SFF_H_ */
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