Ahh, I love coding. Check this out:


// Iterate through this list until all clones are in paths
in_paths = contigs[ctgnum]->num_show;
while ((i < tot) && (in_paths > 0)) {
// Look at both clones
inlist1 = check_inlist(bl[i]->indx1,&c);
inlist2 = check_inlist(bl[i]->indx2,&c);
if (inlist1)
endlist1 = check_endlist(bl[i]->indx1,&c);
if (inlist2)
endlist2 = check_endlist(bl[i]->indx2,&c);

// If both clones are already in the middle of lists
// - yay! do next one
if ((inlist1 && inlist2) && ((!endlist1) && (!endlist2)))
continue;

// If neither clone is in a list
// - make a new list out of these two
if ((!inlist1) && (!inlist2)) {
}

// If one of the clones is the end of a list
// - Add other clone to the end of this list
// Do for indx1
if ((!inlist1) && (endlist2)) {
}

// Do for indx2
if ((!inlist2) && (endlist1)) {
}

// If one of the clones isn't in a list, and other is internal in a list
// - add these clones to appropriate PathItem->link
// Do for indx1
if ((!inlist1) && ((inlist2) && (!endlist2))) {
}

// Do for indx2
if ((!inlist2) && ((inlist1) && (!endlist1))) {
}

}