void addLink(cfuhash_table_t * linkHash,
BM_linkInfo * LI,
int cid1,
int cid2
) {
BM_linkInfo** nextLink_ptr = (BM_linkInfo**) &LI->nextLink;
// see if the key is in the hash already
char * key = calloc(30, sizeof(char)); // allocate room for the key
makeContigKey(key, cid1, cid2);
BM_linkPair * base_LP = cfuhash_get(linkHash, key);
if (base_LP != NULL) {
// exists in the hash -> daisy chain it on
*nextLink_ptr = base_LP->LI;
base_LP->LI = LI;
base_LP->numLinks++;
}
else {
// we'll need to build a bit of infrastructure
// store the contig ids once only
BM_linkPair * LP = (BM_linkPair*) calloc(1, sizeof(BM_linkPair));
if(cid1 < cid2) {
LP->cid1 = cid1;
LP->cid2 = cid2;
}
else {
LP->cid1 = cid2;
LP->cid2 = cid1;
}
LP->LI = LI;
LP->numLinks = 1;
*nextLink_ptr = LI; // point to self means end of list
// finally, add the lot to the hash
cfuhash_put(linkHash, key, LP);
}
if (key != 0) {
free(key);
key = 0;
}
}
void addLink(cfuhash_table_t * linkHash,
int cid_1,
int cid_2,
int pos_1,
int pos_2,
int orient_1,
int orient_2,
int bam_ID
)
{
// store the link info, swap order of cid_1 and cid_2 if needed
PM_link_info* LI = (PM_link_info*) calloc(1, sizeof(PM_link_info));
if(cid_1 < cid_2){
LI->orient_1 = orient_1;
LI->orient_2 = orient_2;
LI->pos_1 = pos_1;
LI->pos_2 = pos_2;
}
else
{
LI->orient_1 = orient_2;
LI->orient_2 = orient_1;
LI->pos_1 = pos_2;
LI->pos_2 = pos_1;
}
LI->bam_ID = bam_ID;
PM_link_info** next_link_ptr = (PM_link_info**) &LI->next_link;
// see if the key is in the hash already
char * key = calloc(30, sizeof(char)); // allocate room for the key
makeContigKey(key, cid_1, cid_2);
PM_link_pair * base_LP = cfuhash_get(linkHash, key);
if (base_LP != NULL)
{
// exists in the hash -> daisy chain it on
*next_link_ptr = base_LP->LI;
base_LP->LI = LI;
base_LP->numLinks++;
}
else
{
// we'll need to build a bit of infrastructure
// store the contig ids once only
PM_link_pair * LP = (PM_link_pair*) calloc(1, sizeof(PM_link_pair));
if(cid_1 < cid_2)
{
LP->cid_1 = cid_1;
LP->cid_2 = cid_2;
}
else
{
LP->cid_1 = cid_2;
LP->cid_2 = cid_1;
}
LP->LI = LI;
LP->numLinks = 1;
*next_link_ptr = LI; // point to self means end of list
// finally, add the lot to the hash
cfuhash_put(linkHash, key, LP);
}
free(key);
}
