comparison srf2fastq/io_lib-1.12.2/man/man3/ExperimentFile.3 @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

0:d901c9f41a6a

.TH ExperimentFile 3 "" "" "Staden Package"

.SH NAME

.LP
.BR exp_read_info ,
.BR exp_fread_info ,
.BR exp_create_info ,
.BR exp_destroy_info ,
.BR exp_create_range ,
.BR exp_extract_range ,
.BR exp_get_feature_index ,
.BR exp_get_int ,
.BR exp_get_rng ,
.BR exp_get_str ,
.BR exp_put_int ,
.BR exp_put_rng ,
.BR exp_put_str ,
.BR exp_print_line ,
.BR exp_print_seq ,
.BR exp_print_file ,
.BR opos2str ,
.BR str2opos ,
.BR conf2str ,
.BR str2conf
\- Manipulations of the Experiment File format

.IX "exp_read_info()" "" "exp_read_info()"
.IX "exp_fread_info()" "" "exp_fread_info()"
.IX "exp_create_info()" "" "exp_create_info()"
.IX "exp_destroy_info()" "" "exp_destroy_info()"
.IX "exp_create_range()" "" "exp_create_range()"
.IX "exp_extract_range()" "" "exp_extract_range()"
.IX "exp_get_feature_index()" "" "exp_get_feature_index()"
.IX "exp_get_int()" "" "exp_get_int()"
.IX "exp_get_rng()" "" "exp_get_rng()"
.IX "exp_get_str()" "" "exp_get_str()"
.IX "exp_put_int()" "" "exp_put_int()"
.IX "exp_put_rng()" "" "exp_put_rng()"
.IX "exp_put_str()" "" "exp_put_str()"
.IX "exp_print_line()" "" "exp_print_line()"
.IX "exp_print_seq()" "" "exp_print_seq()"
.IX "exp_print_file()" "" "exp_print_file()"
.IX "opos2str()" "" "opos2str()"
.IX "str2opos()" "" "str2opos()"
.IX "conf2str()" "" "conf2str()"
.IX "str2conf()" "" "str2conf()"

.SH SYNOPSIS
.LP
.nf
.ft B
#include <expFileIO.h>

.nf
.ft B
Exp_info *exp_read_info(
	char *file);
.ft
.fi
.LP
.nf
.ft B
Exp_info *exp_fread_info(
	FILE *fp);
.ft
.fi
.LP
.nf
.ft B
Exp_info *exp_create_info();
.ft
.fi
.LP
.nf
.ft B
void exp_destroy_info(
	Exp_info *e);
.ft
.fi
.LP
.nf
.ft B
char *exp_create_range(
	char *str,
	int start,
	int end);
.ft
.fi
.LP
.nf
.ft B
int exp_extract_range(
	char *str,
	int *start,
	int *end);
.ft
.fi
.LP
.nf
.ft B
int exp_get_feature_index(
	char *e);
.ft
.fi
.LP
.nf
.ft B
int exp_get_int(
	Exp_info *e,
	int id,
	int *val);
.ft
.fi
.LP
.nf
.ft B
int exp_get_rng(
	Exp_info *e,
	int id,
	int *from,
	int *to);
.ft
.fi
.LP
.nf
.ft B
int exp_get_str(
	Exp_info *e,
	int id,
	char *s,
	f_implicit s_l);
.ft
.fi
.LP
.nf
.ft B
int exp_put_int(
	Exp_info *e,
	int id,
	int *val);
.ft
.fi
.LP
.nf
.ft B
int exp_put_rng(
	Exp_info *e,
	int id,
	int *from,
	int *to);
.ft
.fi
.LP
.nf
.ft B
int exp_put_str(
	Exp_info *e,
	int id,
	char *s,
	f_implicit s_l);
.ft
.fi
.LP
.nf
.ft B
int exp_print_line(
	FILE *fp,
	Exp_info *e,
	int eflt,
	int i);
.ft
.fi
.LP
.nf
.ft B
int exp_print_seq(
	FILE *fp,
	Exp_info *e,
	int eflt,
	int i);
.ft
.fi
.LP
.nf
.ft B
void exp_print_file(
	FILE *fp,
	Exp_info *e);
.ft
.fi
.LP
.nf
.ft B
char *opos2str(
	int2 *opos,
	int len,
	char *buf);
.ft
.fi
.LP
.nf
.ft B
int str2opos(
	int2 *opos,
	char *buf);
.ft
.fi
.LP
.nf
.ft B
char *conf2str(
	int1 *conf,
	int len,
	char *buf);
.ft
.fi
.LP
.nf
.ft B
int str2conf(
	int1 *conf,
	char *buf);
.ft
.fi

.SH DESCRIPTION
.LP
These functions manipulate Experiment Files. They include functions for
reading, writing, and editing the files. The principle structure used by the
routines is the \fBExp_info\fR structure. This is as follows.
.EX 5
.ft B
#define MAXIMUM_EFLT_LENGTH     4
#define MAXIMUM_EFLTS          48
#define EXP_FILE_LINE_LENGTH  128

typedef Array Exp_entries;

typedef struct {
    Array entries[MAXIMUM_EFLTS]; /* array of array of entries */
    int Nentries[MAXIMUM_EFLTS];  /* array of number of entries */
    FILE *fp;
} Exp_info;

#define NULL_Exp_info ( (Exp_info *) NULL )
.ft
.EE
.LP
For the purposes of simple and efficient coding, each line on an experiment
file must be smaller than the defined EXP_FILE_LINE_LENGTH, which is 128
characters.
.LP
Many functions take an experiment file line type identifier as an argument.
These functions are listed in the prototypes as taking \fBint id\fR. Here
\fBid\fR should be specified using one of the macros defining in the header
file. They take the form of \fBEFLT_\fRXX where XX is the line type. For
instance, the \fBID\fR line type identifier should be written as
\fBEFLT_ID\fR.
.LP
The C functions available follow. Some FORTRAN interfaces are also available,
but these are not documented. See the include file for their prototypes.
.LP
.B exp_read_info
and
.B exp_fread_info
read an experiment file into an allocated \fBExp_info\fR structure. If
successful, the structure pointer is return. Otherwise the null pointer is
returned.
.LP
.B exp_create_info
allocates and initialises a new, blank, \fBExp_info\fR structure. If
successful, the structure pointer is return. Otherwise the null pointer is
returned.
.LP
.B exp_destroy_info
deallocates an \fBExp_info\fR structure.
.LP
.B exp_create_range
creates a string using the experiment file range format of "start..stop". This
format is used by the AQ, ON, TG and TC line types. The buffer specified
should be large enough to hold the string. The function returns the \fBstr\fR
pointer supplied as an argument.
.LP
.B exp_extract_range
extracts the start and end values from the string representation of a range;
"start..stop". The values are stored in the integer pointers sent as
arguments. If successful, the function returns 0. Otherwise -1 is returned.
.LP
.B exp_get_feature_index
converts from a string representation of an experiment file line type to the
integer value. For example, \fBexp_get_feature_index("SQ")\fR returns the
integer 22, which is the same as the \fBEFLT_SQ\fR definition.
.LP
.B exp_get_int
obtains the integer value held in a specific line type. The value is stored in
the integer pointer \fBval\fR. If successful, the function returns 0.
Otherwise 1 is returned.
.LP
.B exp_get_rng
obtains the range values held in a specific line type. The values are stored in
the integer pointers \fBfrom\fR and \fBto\fR. If successful, the function
returns 0. Otherwise 1 is returned.
.LP
.B exp_get_str
obtains the string value held in a specific line type. The value is stored in
the string \fBs\fR. At most \fBs_l\fR characters are copied. If successful,
the function returns 0. Otherwise 1 is returned.
.LP
.B exp_put_int
writes the integer pointed to by \fBval\fR to the specified line type. If
successful, the function returns 0. Otherwise 1 is returned.
.LP
.B exp_put_rng
writes the range pointed to by \fBfrom\fR and \fBto\fR to the specified line
type. If successful, the function returns 0. Otherwise 1 is returned.
.LP
.B exp_put_str
writes the string \fBs\fR of length \fBs_l\fR to the specified line type. If
successful, the function returns 0. Otherwise 1 is returned.
.LP
.B exp_print_line
outputs all entries of the specified type to the specified file pointer.
.LP
.B exp_print_seq
.LP
.B exp_print_file
outputs all entries of all line types to the specified file pointer.
.LP
.B opos2str
converts an array of original positions held in \fBopos\fR with \fBlen\fR
elements to a string suitable for use in the ON line type. The \fBbuf\fR
should be large enough to hold the string, which in the worst case will be
4 * sequence length. Returns \fBbuf\fR.
.LP
.B str2opos
converts the experiment file original position string held in \fBbuf\fR to an
array of original positions to be stored in \fBopos\fR. \fBopos\fR must be
large enough to hold the data, hence it should be of the same length as the
sequence. Returns the number of elements written to the \fBopos\fR array.
.LP
.B conf2str
converts an array of confidence values helf in \fBconf\dR with \fBlen\fR
elements to a string suitable for use in the AV line type. The \fBbuf\fR
should be large enough to hold the string, which in the worst case will be
4 * sequence length. Returns \fBbuf\fR.
.LP
.B str2conf
convers the experiment file confidence values string held in \fBbuf\fR to an
array of confidence values to be stored in \fBconf\fR. \fBconf\fR must be
large enough to hold the data, hence it should be of the same length as the
sequence. Returns the number of elements written to the \fBconf\fR array.

.SH SEE ALSO
.LP
.BR ExperimentFile (4)