int bode::DensitySet::lsearch(std::vector<struct IntervalIndex> &v,int left,int right) {
int pos,top;
top = v.size();
for (pos=0;pos<top;pos++) {
if (olap(v[pos],left,right)) {
return pos;
}
}
return -1;
}
void bode::DensitySet::add(std::string &chrom,int left,int right) {
int i;
int top;
if (chrom2intervals.count(chrom) == 0) {
return;
}
std::vector<struct IntervalIndex>& vii = chrom2intervals[chrom];
top = vii.size();
i = bsearch(vii,left,right);
while (i != -1 && i < top && olap(vii[i],left,right)) {
intervals[vii[i].index].dmap->set(left - vii[i].left,right - vii[i].left);
i++;
}
}
void
Read_Olaps(coParameters *G, gkStore *gkpStore) {
ovStore *ovs = new ovStore(G->ovlStorePath, gkpStore);
ovs->setRange(G->bgnID, G->endID);
uint64 numolaps = ovs->numOverlapsInRange();
uint64 numNormal = 0;
uint64 numInnie = 0;
fprintf(stderr, "Read_Olaps()-- Loading "F_U64" overlaps from '%s' for reads "F_U32" to "F_U32"\n",
numolaps, G->ovlStorePath, G->bgnID, G->endID);
fprintf(stderr, "--Allocate "F_U64" MB for overlaps.\n",
(sizeof(Olap_Info_t) * numolaps) >> 20);
G->olaps = new Olap_Info_t [numolaps];
G->olapsLen = 0;
ovOverlap olap(gkpStore);
while (ovs->readOverlap(&olap)) {
G->olaps[G->olapsLen].a_iid = olap.a_iid;
G->olaps[G->olapsLen].b_iid = olap.b_iid;
G->olaps[G->olapsLen].a_hang = olap.a_hang();
G->olaps[G->olapsLen].b_hang = olap.b_hang();
//G->olaps[G->olapsLen].orient = (olap.flipped()) ? INNIE : NORMAL;
G->olaps[G->olapsLen].innie = (olap.flipped() == true);
G->olaps[G->olapsLen].normal = (olap.flipped() == false);
G->olaps[G->olapsLen].order = G->olapsLen;
G->olaps[G->olapsLen].evalue = olap.evalue();
numNormal += (G->olaps[G->olapsLen].normal == true);
numInnie += (G->olaps[G->olapsLen].innie == true);
G->olapsLen++;
}
delete ovs;
fprintf(stderr, "Read_Olaps()-- Loaded "F_U64" overlaps -- "F_U64" normal and "F_U64" innie.\n",
G->olapsLen, numNormal, numInnie);
}
int bode::DensitySet::bsearch(std::vector<struct IntervalIndex> &v,int left,int right) {
int top,bot,mid;
bot = 0;
top = v.size() - 1;
while (bot < top) {
mid = (bot+top)/2;
if (v[mid].right < left) {
bot = mid+1;
} else {
top = mid;
}
}
if (top == bot && olap(v[bot],left,right)) {
return bot;
} else {
return -1;
}
}