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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	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  deallo-
       cate 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 cor-
       ret format type by analysing the	trace file for magic numbers and  com-
       position.  The format field of the structure can	then be	used to	deter-
       mine 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 re-
       sulting 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() func-
       tions 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)

NAME | SYNOPSIS | DESCRIPTION | RETURN VALUES | SEE ALSO

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