split_contig_tags

#include <tagUtils.h>

void split_contig_tags(
        GapIO  *io,
        int     cont1,
        int     cont2,
        int     posl,
        int     posr);

This function is called by the break contig algorithm and has little, if any, other use. When we're splitting a contig in half we need to move the annotations too. Annotations that overlap the two contigs are duplicated. Annotations that overlap the end of a contig have their lengths and positions corrected.

posl and posr hold the overlap region of contigs cont1 and cont2 before splitting. At the time of calling this routine, cont2 has just been created (and has no tags). Both contigs have their lengths set correctly, but all of the tags are still in cont1. This function corrects these tag locations.