void printLinkPair(PM_link_pair* LP, char ** bamNames, char ** contigNames)
{
printf("===\n(%s, %s, %d links)\n", contigNames[LP->cid_1], contigNames[LP->cid_2], LP->numLinks);
PM_link_info* LI = LP->LI;
do {
printf("\t");
printLinkInfo(LI, bamNames);
printf("\n");
} while(getNextLinkInfo(&LI));
}
int stepLinkWalker(BM_LinkWalker * walker) {
if(getNextLinkInfo(&(walker->LI))) {
// still on the same pair
return 1;
}
else {
// at the end of the links of this contig pair
walker->keyCount += 1;
if(walker->keyCount < walker->numKeys) {
walker->pair = cfuhash_get(walker->linkHash,
walker->keys[walker->keyCount]);
if (walker->keys[walker->keyCount] != 0) {
free(walker->keys[walker->keyCount]);
walker->keys[walker->keyCount] = 0;
}
walker->LI = (walker->pair)->LI;
return 2;
}
}
return 0;
}
