tag_shift_for_insert

#include <tagUtils.h>

void tag_shift_for_insert(
        GapIO  *io,
        int     N,
        int     pos);

This function shifts or extends tags by a single base. The purpose is to handle cases where we need to insert into a sequence. An edit at position pos will mean moving every tag to the right of this one base rightwards. A tag that spans position pos will have it's length increased by one. If N is positive it specifies the reading number to operate on, otherwise it specifies the contig number (negated).

NOTE: This function does not work correctly for complemented readings. It is planned to fix this problem by creating a new function that operates in a more intelligent fashion. To work around this problem, logic similar to the following needs to be used.

    /*
     * Adjust tags
     * NOTE: Must always traverse reading in reverse of original sense
     */
    if (complemented) {
        for(i=j=0; i < gel_len; i++) {
            if (orig_seq[i] != padded_seq[j]) {
                tag_shift_for_insert(io, gel_num, length-j);
            } else
                j++;
        }
    } else {
        for(i=j=gel_len-1; i >= 0; i--) {
            if (orig_seq[i] != padded_seq[j]) {
                tag_shift_for_insert(io, gel_num, j+1);
            } else
                j--;
        }
    }

In the above example padded_seq is a padded copy of orig_seq. The function calls tag_shift_for_insert for each pad. Note that the order of the insertions is important and differs depending on whether the reading is complemented or not.