read_reading(3) 						  Staden Package						   read_reading(3)

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 struc-
       ture. 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)

																   read_reading(3)