/usr/include/io_lib/Read.h is in libstaden-read-dev 1.12.4-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* Copyright (c) Medical Research Council 1994. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written by James Bonfield, Simon Dear, Rodger Staden,
* as part of the Staden Package at the MRC Laboratory of Molecular
* Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*/
#ifndef _Read_h_
#define _Read_h_
/*
* Title: Read
*
* File: Read.h
* Purpose: Read data type
* Last update: June 14 1994
*/
/*
* This module encodes the `Read' sequence data structure.
*
* A `Read' contains information about bases and traces which are laid
* out along a single dimension of points. The number of points in a
* paricular sequence is given by `getNPoints', and these are numbered
* 0..getNPoints-1. At each point there are four trace readings, one
* for each base.
*
* The number of bases is `getNBases' which are numbered 0..N-1.
* Bases are represented by `char's. Every base is located at a
* particular point.
*
* The behaviour of these routines is undefined if given NULLRead or
* an undefined sequence.
*/
#include "io_lib/os.h"
#include "io_lib/scf.h"
#include "io_lib/mFILE.h"
#ifdef __cplusplus
extern "C" {
#endif
/*
*-----------------------------------------------------------------------------
* Macros
*-----------------------------------------------------------------------------
*/
#define NULLRead ((Read *)NULL)
/* Trace file formats */
#define TT_ERR -1
#define TT_UNK 0
#define TT_SCF 1
#define TT_ABI 2
#define TT_ALF 3
#define TT_PLN 4
#define TT_EXP 5
#define TT_CTF 6
#define TT_ZTR 7
#define TT_ZTR1 8
#define TT_ZTR2 9
#define TT_ZTR3 10
#define TT_BIO 11
#define TT_SFF 12
#define TT_ANY TT_UNK
/* ANYTR is specifically any *trace* type and not EXP or PLN format */
#define TT_ANYTR 13
#define READ_BASES (1<<0)
#define READ_SAMPLES (1<<1)
#define READ_COMMENTS (1<<2)
#define READ_ALL (READ_BASES | READ_SAMPLES | READ_COMMENTS)
/*
*-----------------------------------------------------------------------------
* Structures and typedefs
*-----------------------------------------------------------------------------
*/
typedef uint_2 TRACE; /* for trace heights */
typedef struct
{
int format; /* Trace file format */
char *trace_name; /* Trace file name */
int NPoints; /* No. of points of data */
int NBases; /* No. of bases */
/* Traces */
TRACE *traceA; /* Array of length `NPoints' */
TRACE *traceC; /* Array of length `NPoints' */
TRACE *traceG; /* Array of length `NPoints' */
TRACE *traceT; /* Array of length `NPoints' */
TRACE maxTraceVal; /* The maximal value in any trace */
int baseline; /* The zero offset for TRACE values */
/* Bases */
char *base; /* Array of length `NBases' */
uint_2 *basePos; /* Array of length `NBases' */
/* Cutoffs */
int leftCutoff; /* Number of unwanted bases */
int rightCutoff; /* First unwanted base at right end */
/* Miscellaneous Sequence Information */
char *info; /* misc seq info, eg comments */
/* Probability information */
char *prob_A; /* Array of length 'NBases' */
char *prob_C; /* Array of length 'NBases' */
char *prob_G; /* Array of length 'NBases' */
char *prob_T; /* Array of length 'NBases' */
/* The original input format data, or NULL if inapplicable */
int orig_trace_format;
void (*orig_trace_free)(void *ptr);
void *orig_trace;
char *ident; /* Seq id, NULL for unknown. Malloced data.
Owned and freed by io_lib. */
/* Pyrosequencing "peaks" (more like spikes). NULL if not used */
int nflows; /* Number of "flows" */
char *flow_order; /* Bases flowed across */
float *flow; /* Processed to be 1 base unit oriented */
unsigned int*flow_raw; /* Unprocessed data */
void *private_data; /* The 'private data' block and size from SCF, */
int private_size; /* NULL & 0 if not present. */
} Read;
/*
*-----------------------------------------------------------------------------
* Function prototypes
*-----------------------------------------------------------------------------
*/
/* ----- Main I/O routines ----- */
/*
* Read a sequence from a file "fn" of format "format". If "format" is 0
* (TT_ANY), we automatically determine the correct format.
*
* Returns:
* Read * for success
* NULLRead for failure
*/
Read *read_reading(char *fn, int format);
Read *fread_reading(FILE *fp, char *fn, int format);
Read *mfread_reading(mFILE *fp, char *fn, int format);
/*
* Write a sequence to a file "fn" of format "format". If "format" is 0,
* we choose our favourite - SCF.
*
* Returns:
* 0 for success
* -1 for failure
*/
int write_reading(char *fn, Read *read, int format);
int fwrite_reading(FILE *fp, Read *read, int format);
int mfwrite_reading(mFILE *fp, Read *read, int format);
/* ----- Utility routines ----- */
/*
* Allocate a new sequence, with the given sizes.
* Returns:
* "Read *" for success
* "NULLRead" for failure
*/
Read *read_allocate(int num_points, int num_bases);
/*
* Duplicates the read structure and optionally gives it a new filename.
* The following fields are not duplicated:
*
* int orig_trace_format;
* void (*orig_trace_free)(void *ptr);
* void *orig_trace;
* char *ident;
*
* Returns:
* "Read *" for success
* "NULLRead" for failure
*/
Read* read_dup( Read* src, const char* new_name );
/*
* Free memory allocated to a sequence by read_allocate().
*/
void read_deallocate(Read *read);
/* unix specific file deletion routine */
int remove_file(char *fn);
Read *read_abi(char *fn);
Read *fread_abi(FILE *fp);
Read *mfread_abi(mFILE *fp);
int write_abi(char *fn, Read *read);
int fwrite_abi(FILE *fp, Read *read);
int mfwrite_abi(mFILE *fp, Read *read);
int write_alf(char *fn, Read *read);
int fwrite_alf(FILE *fp, Read *read);
int mfwrite_alf(mFILE *fp, Read *read);
Read *read_alf(char *fn);
Read *fread_alf(FILE *fp);
Read *mfread_alf(mFILE *fp);
int write_pln(char *fn, Read *read);
int fwrite_pln(FILE *fp, Read *read);
int mfwrite_pln(mFILE *fp, Read *read);
Read *read_pln(char *fn);
Read *fread_pln(FILE *fp);
Read *mfread_pln(mFILE *fp);
Read *read_ctf(char *fn);
Read *fread_ctf(FILE *fp);
Read *mfread_ctf(mFILE *fp);
int write_ctf(char *fn, Read *read);
int fwrite_ctf(FILE *fp, Read *read);
int mfwrite_ctf(mFILE *fp, Read *read);
int read_sections(int sec);
#include "io_lib/translate.h"
#include "io_lib/compress.h"
#ifdef __cplusplus
}
#endif
#endif /* _Read_h_ */
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