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       read_reading,  fread_reading - Read a trace file into a Read structure.


       #include <Read.h>

       Read *read_reading(
            char *filename,
            int format);

       Read *fread_reading(
            FILE *fp,
            char *filename,
            int format);


       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 lengthNPoints*/
           TRACE      *traceC;      /* Array of lengthNPoints*/
           TRACE      *traceG;      /* Array of lengthNPoints*/
           TRACE      *traceT;      /* Array of lengthNPoints*/
           TRACE       maxTraceVal; /* The maximal value in any trace */

           /* Bases */
           char       *base;        /* Array of lengthNBases*/
           uint_2     *basePos;     /* Array of lengthNBases*/

           /* 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 lengthNBases*/
           char       *prob_C;      /* Array of lengthNBases*/
           char       *prob_G;      /* Array of lengthNBases*/
           char       *prob_T;      /* Array of lengthNBases*/

           /* The original input format data, or NULL if inapplicable */
           int orig_trace_format;
           void *orig_trace;

       } Read;


       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).


       write_reading(3), fwrite_reading(3), deallocate_reading(3), scf(4),