Read (4)

#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 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;

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),

ExperimentFile(4)