/** Query VCF entries intersecting 'marker' at node 'idx' */
protected void queryIntersects(Interval queryMarker, int idx, Markers results) {
if (intersectFilePosStart[idx] == null) return;
if (debug) Gpr.debug("queryIntersects\tidx: " + idx);
// Read entries from disk
List<VcfEntry> vcfEntries = readEntries(idx);
// Find matching entries
for (VcfEntry ve : vcfEntries) {
// If any variant within the vcfEntry intersects the query
// marker, we store this VCF entry as a result
for (Variant var : ve.variants()) {
if (var.intersects(queryMarker)) {
if (debug) Gpr.debug("\tAdding matching result: " + ve);
results.add(ve);
break; // Store this entry only once
}
}
// Past query's end coordinate? We don't need to look any further
if (queryMarker.getEnd() < ve.getStart()) return;
}
}
