1read_reading(3)                 Staden Package                 read_reading(3)
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NAME

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

10       #include <Read.h>
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12       Read *read_reading(
13            char *filename,
14            int format);
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16       Read *fread_reading(
17            FILE *fp,
18            char *filename,
19            int format);
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DESCRIPTION

23       These  functions  read  trace files into a Read structure. A variety of
24       formats are supported including ABI, ALF and SCF. (Note that the  first
25       two  are  only supported when the library is used as part of the Staden
26       Package.)  Additionally, support for reading  the  plain  (old)  staden
27       format  files  and Experiment files is included. Compressed trace files
28       may also be read.  Decompression is performed using either gzip  -d  or
29       uncompress  and  is written to a temporary file for further processing.
30       The temporary file is then read and removed.
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32       When reading an experiment file the trace file referenced by the LN and
33       LT  line  types  is read. The QL, QR (left and right quality clips), SL
34       and SR (left and right vector clips) are taken from the Experiment file
35       to  produce  the cutoff information held within the Read structure. The
36       orig_trace field of the Read structure will then contain the pointer to
37       the  experiment  file structure and the orig_trace_format field will be
38       set to TT_EXP.
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40       The functions allocate a Read structure which is returned.  To  deallo‐
41       cate this structure use the read_deallocate() function.
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43       read_reading()  reads  a  trace from the specified filename and format.
44       Formats available are TT_SCF, TT_ABI, TT_ALF, TT_PLN, TT_EXPand TT_ANY.
45       Specifying  format TT_ANY will attempt to automatically detect the cor‐
46       ret format type by analysing the trace file for magic numbers and  com‐
47       position.  The format field of the structure can then be used to deter‐
48       mine the real trace type.
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50       fread_reading() reads a trace from  the  specified  file  pointer.  The
51       filename  argument  is  used  for  setting  the trace_name field of the
52       resulting structure, and for error messages. Otherwise the function  is
53       identical to the read_reading() function.
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55       The Read structure itself is as follows.
56       typedef uint_2 TRACE;        /* for trace heights */
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58       typedef struct
59       {
60           int         format;      /* Trace file format */
61           char       *trace_name;  /* Trace file name   */
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63           int         NPoints;     /* No. of points of data */
64           int         NBases;      /* No. of bases          */
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66           /* Traces */
67           TRACE      *traceA;      /* Array of length `NPoints' */
68           TRACE      *traceC;      /* Array of length `NPoints' */
69           TRACE      *traceG;      /* Array of length `NPoints' */
70           TRACE      *traceT;      /* Array of length `NPoints' */
71           TRACE       maxTraceVal; /* The maximal value in any trace */
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73           /* Bases */
74           char       *base;        /* Array of length `NBases' */
75           uint_2     *basePos;     /* Array of length `NBases' */
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77           /* Cutoffs */
78           int         leftCutoff;  /* Number of unwanted bases */
79           int         rightCutoff; /* Number of unwanted bases */
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81           /* Miscellaneous Sequence Information */
82           char       *info;        /* misc seq info, eg comments */
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84           /* Probability information */
85           char       *prob_A;      /* Array of length 'NBases' */
86           char       *prob_C;      /* Array of length 'NBases' */
87           char       *prob_G;      /* Array of length 'NBases' */
88           char       *prob_T;      /* Array of length 'NBases' */
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90           /* The original input format data, or NULL if inapplicable */
91           int orig_trace_format;
92           void *orig_trace;
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94       } Read;
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RETURN VALUES

97       On  successful completion, the read_reading() and fread_reading() func‐
98       tions return a pointer to a Read structure. Otherwise  these  functions
99       return NULLRead (which is a null pointer).
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SEE ALSO

103       write_reading(3), fwrite_reading(3), deallocate_reading(3), scf(4),
104       ExperimentFile(4)
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108                                                               read_reading(3)
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