NAME¶
read_reading,
fread_reading - Read a trace file into a
Read
structure.
SYNOPSIS¶
#include <Read.h>
Read *read_reading(
char *filename,
int format);
Read *fread_reading(
FILE *fp,
char *filename,
int format);
DESCRIPTION¶
These functions read trace files into a
Read 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
gzip -d or
uncompress
and is written to a temporary file for further processing. The temporary file
is then read and removed.
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
Read structure. The
orig_trace field
of the
Read structure will then contain the pointer to the experiment
file structure and the
orig_trace_format field will be set to
TT_EXP.
The functions allocate a
Read structure which is returned. To deallocate
this structure use the
read_deallocate() function.
read_reading() reads a trace from the specified filename and format.
Formats available are
TT_SCF,
TT_ABI,
TT_ALF,
TT_PLN,
TT_EXPand
TT_ANY. Specifying format
TT_ANY
will attempt to automatically detect the corret format type by analysing the
trace file for magic numbers and composition. The
format field of the
structure can then be used to determine the real trace type.
fread_reading() reads a trace from the specified file pointer. The
filename argument is used for setting the
trace_name field of the
resulting structure, and for error messages. Otherwise the function is
identical to the
read_reading() function.
The
Read structure itself is as follows.
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;
RETURN VALUES¶
On successful completion, the
read_reading() and
fread_reading()
functions return a pointer to a
Read structure. Otherwise these
functions return NULLRead (which is a null pointer).
SEE ALSO¶
write_reading(3),
fwrite_reading(3),
deallocate_reading(3),
scf(4),
ExperimentFile(4)