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#include <IO.h>

int io_replace_seq(
        int2    maxgel,
        int2   *length,
        int2   *start,
        int2   *end,
        char   *seq,
        int1   *conf,
        int2   *opos,
        int2    pos,
        char   *bases,
        int1   *newconf,
        int2   *newopos,
        int2    Nbases,
        int     diff_only,
        int     conf_only);

io_replace_seq replaces on or more bases from the sequence, confidence and original positions arrays specified. No database I/O is performed.

The existing sequence, confidence values, and original positions arrays are passed as seq, conf, and opos arguments. All are mandatory. The length of sequence and hence the number of used elements in these arrays is passed as length, with start and end containing the left and right cutoff positions. The allocated size of these arrays is maxgel. FIXME: it is used - does it need to be?

The new sequence, confidence values, and original positions to replace are passed as bases, newconf and newopos. The number of bases to replace is NBases. Either or both of the newconf and newopos arguments may be NULL. The replaced confidence values will then default to 100 for non pad ("*") bases. For pads, the confidence value defaults to the average of the confidence values of the first two neighbouring bases that are not pads. The replaced original positions default to 0. These bases are to be inserted at the position specified by pos, counting as position 1 being to the left of the first base in the sequence. The length, start and end values are left unchanged.

This function returns 0 for success.

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This page is maintained by staden-package. Last generated on 1 March 2001.