annotate srf2fastq/io_lib-1.12.2/man/man3/read_reading.3 @ 0:d901c9f41a6a default tip

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

.TH read_reading 3 "" "" "Staden Package"

.SH NAME

.LP
.BR read_reading ,
.BR fread_reading
\- Read a trace file into a \fBRead\fR structure.

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

.nf
.ft B
Read *read_reading(
	char *filename,
	int format);
.ft
.fi
.LP
.nf
.ft B
Read *fread_reading(
	FILE *fp,
	char *filename,
	int format);
.ft
.fi
.IX "read_reading()" "" "read_reading()"
.IX "fread_reading()" "" "fread_reading()"

.SH DESCRIPTION
.LP
These functions read trace files into a \fBRead\fR structure. A variety of
formats are supported including ABI, ALF and SCF. (Note that the first two are
only supported when the library is used as part of the Staden Package.)
Additionally, support for reading the plain (old) staden format files and
Experiment files is included. Compressed trace files may also be read.
Decompression is performed using either \fBgzip -d\fR or \fBuncompress\fR and
is written to a temporary file for further processing. The temporary file is
then read and removed.
.LP
When reading an experiment file the trace file referenced by the LN and LT
line types is read. The QL, QR (left and right quality clips), SL and SR
(left and right vector clips) are taken from the Experiment file to produce
the cutoff information held within the \fBRead\fR structure. The
\fBorig_trace\fR field of the \fBRead\fR structure will then contain the
pointer to the experiment file structure and the \fBorig_trace_format\fR field
will be set to \fBTT_EXP\fR.
.LP
The functions allocate a \fBRead\fR structure which is returned. To deallocate
this structure use the \fBread_deallocate()\fR function.
.LP
.B read_reading()
reads a trace from the specified filename and format. Formats available are
.BR TT_SCF ,
.BR TT_ABI ,
.BR TT_ALF ,
.BR TT_PLN ,
.BR TT_EXP and
.BR TT_ANY .
Specifying format \fBTT_ANY\fR will attempt to automatically detect the corret
format type by analysing the trace file for magic numbers and composition. The
\fBformat\fR field of the structure can then be used to determine the real
trace type.
.LP
.B fread_reading()
reads a trace from the specified file pointer. The filename argument is used
for setting the \fBtrace_name\fR field of the resulting structure, and for
error messages. Otherwise the function is identical to the
\fBread_reading()\fR function.
.LP
The \fBRead\fR structure itself is as follows.
.EX 5
.ft B
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 */

    /* Bases */
    char       *base;        /* Array of length `NBases' */
    uint_2     *basePos;     /* Array of length `NBases' */

    /* Cutoffs */
    int         leftCutoff;  /* Number of unwanted bases */
    int         rightCutoff; /* Number of unwanted bases */

    /* 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;

} Read;
.EE
.ft
.LP

.SH RETURN VALUES
.LP
On successful completion, the \fBread_reading()\fR and \fBfread_reading()\fR
functions return a pointer to a \fBRead\fR structure. Otherwise these
functions return NULLRead (which is a null pointer).

.SH SEE ALSO
.LP
.BR write_reading (3),
.BR fwrite_reading (3),
.BR deallocate_reading (3),
.BR scf (4),
.br
.BR ExperimentFile (4)