/**
* Set all parameters in one 'row'
*
* <p>WARNIGN: If we don't do it this way, we get strange errors due to array resizing (array
* appears to be filled with zeros after being set)
*/
void set(int idx, int leftIdx, int rightIdx, int midPos, TIntArrayList intersecting) {
// Assign values
left[idx] = leftIdx;
right[idx] = rightIdx;
mid[idx] = midPos;
// Assign intersecting values
if (intersecting.isEmpty()) {
intersectFilePosStart[idx] = intersectFilePosEnd[idx] = null;
} else {
// First try to collapse intersecting all intervals as a single file block
if (intersecting.size() > 0 && consecutiveFileBlock(intersecting)) {
// OK, we can collapse all entries into a file block
intersectFilePosStart[idx] = new long[1];
intersectFilePosEnd[idx] = new long[1];
intersectFilePosStart[idx][0] = consecutiveFileBlockMin(intersecting);
intersectFilePosEnd[idx][0] = consecutiveFileBlockMax(intersecting);
} else {
// Add entries individually
intersectFilePosStart[idx] = new long[intersecting.size()];
intersectFilePosEnd[idx] = new long[intersecting.size()];
for (int i = 0; i < intersecting.size(); i++) {
int j = intersecting.get(i);
intersectFilePosStart[idx][i] = vcfIndexChromo.getFilePosStart(j);
intersectFilePosEnd[idx][i] = vcfIndexChromo.getFilePosEnd(j);
}
}
}
}
@Override
public void build() {
TIntArrayList idxs = new TIntArrayList(vcfIndexChromo.size());
for (int i = 0; i < vcfIndexChromo.size(); i++) idxs.add(i);
build(idxs);
inSync = true;
}
long consecutiveFileBlockSize(TIntArrayList idxs) {
long max = -1;
long min = Long.MAX_VALUE;
for (int i = 0; i < idxs.size(); i++) {
int idx = idxs.get(i);
min = Math.min(min, vcfIndexChromo.getFilePosStart(idx));
max = Math.max(max, vcfIndexChromo.getFilePosEnd(idx));
}
return max - min;
}
/**
* 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);
}
/** Are entries indexed by 'idxs' consecutive position in the file? */
boolean consecutiveFileBlock(TIntArrayList idxs) {
long end = -1;
for (int i = 0; i < idxs.size(); i++) {
int idx = idxs.get(i);
if (end < 0) end = vcfIndexChromo.getFilePosEnd(idx);
long start = vcfIndexChromo.getFilePosStart(idx);
if ((start - end) > 0) return false;
// Prepare for next iteration
end = vcfIndexChromo.getFilePosEnd(idx);
}
return true;
}
long consecutiveFileBlockMax(TIntArrayList idxs) {
long max = -1;
for (int i = 0; i < idxs.size(); i++) {
int idx = idxs.get(i);
max = Math.max(max, vcfIndexChromo.getFilePosEnd(idx));
}
return max;
}
@SuppressWarnings("unchecked")
public VcfIndexTree(VcfFileIterator vcf, VcfIndexDataChromo vcfIndexChromo) {
this.vcfIndexChromo = vcfIndexChromo;
chromosome = (vcfIndexChromo != null ? vcfIndexChromo.getChromosome() : null);
left = new int[INITIAL_CAPACITY];
right = new int[INITIAL_CAPACITY];
mid = new int[INITIAL_CAPACITY];
intersectFilePosStart = new long[INITIAL_CAPACITY][];
intersectFilePosEnd = new long[INITIAL_CAPACITY][];
intersect = new List[INITIAL_CAPACITY];
size = 0;
}
/** Find all interval indexes from intervals within [startIdx, endIdx] that intersect 'pos' */
int[] intersectIndexes(int startIdx, int endIdx, int pos) {
List<Integer> list = null;
// Find all intersecting intervals
for (int idx = startIdx; idx <= endIdx; idx++) {
if (vcfIndexChromo.intersects(idx, pos)) {
// Add this position
if (list == null) list = new ArrayList<>();
list.add(idx);
}
}
// No results
if (list == null) return new int[0];
// Create an array
int i = 0;
int ints[] = new int[list.size()];
for (int idx : list) ints[i++] = idx;
return ints;
}
@Override
public boolean isEmpty() {
return vcfIndexChromo.size() <= 0;
}
