/**
* Index entries in VcfIndexDataChromo
*
* @return Index of added item (-1 if no item was added)
*/
int build(TIntArrayList idxs) {
if (idxs.isEmpty()) return -1;
// Find middle position
// Note:If we mode the 'mid' point by one base, the probability of intersecting
// an interval is significantly reduced (most entries are SNPs). This reduces
// the index size, the number of 'file.seek()' operations and speeds up the index.
int center = mean(idxs);
int firstStart = vcfIndexChromo.getStart(idxs.get(0));
if (center > firstStart) center--;
// Index of entry to be added
int idx = nextEntry();
// Split indexes into left, right and intersecting
TIntArrayList left = new TIntArrayList();
TIntArrayList right = new TIntArrayList();
TIntArrayList intersecting = new TIntArrayList();
// Try to collapse consecutive entries if there are only a few (i.e. less
// than COLLAPSE_MAX_NUM_ENTRIES) or the block size is small (less
// than COLLAPSE_MAX_BLOCK_SIZE bytes)
if (consecutiveFileBlock(idxs)
&& //
((idxs.size() < COLLAPSE_MAX_NUM_ENTRIES)
|| (consecutiveFileBlockSize(idxs) < maxBlockSize)) //
) {
// Too few intervals forming a consecutive block?
// Just add them to the intersect
for (int i = 0; i < idxs.size(); i++) {
int j = idxs.get(i);
intersecting.add(j);
}
} else {
// Add indexes into left, right and intersecting
for (int i = 0; i < idxs.size(); i++) {
int j = idxs.get(i);
if (vcfIndexChromo.getEnd(j) < center) left.add(j);
else if (vcfIndexChromo.getStart(j) > center) right.add(j);
else intersecting.add(j);
}
}
// Recurse
int leftIdx = build(left);
int rightIdx = build(right);
// Create this entry
set(idx, leftIdx, rightIdx, center, intersecting);
return idx;
}
/** Mean coordinates from entries indexed by 'idxs' */
int mean(TIntArrayList idxs) {
if (idxs.isEmpty()) return 0;
TIntArrayList coordinates = new TIntArrayList(2 * idxs.size());
for (int i = 0; i < idxs.size(); i++) {
int idx = idxs.get(i);
coordinates.add(vcfIndexChromo.getStart(idx));
coordinates.add(vcfIndexChromo.getEnd(idx));
}
coordinates.sort();
return coordinates.get(coordinates.size() / 2);
}
