org.geneweaver.io.connector.OverlapService Maven / Gradle / Ivy
package org.geneweaver.io.connector;
import org.geneweaver.domain.Located;
import org.geneweaver.domain.Overlap;
import org.geneweaver.io.CLI;
/**
* This class contains the raw mathematics for an intersection,
* however iterating all peaks (~100mill) for all variants (~1bill)
* is not going to be scalable.
*
* @author gerrim
*
*/
public class OverlapService {
private ChromosomeService cservice = ChromosomeService.getInstance();
private static final int baseSize = Integer.parseInt(System.getenv().getOrDefault("BASE_SIZE", "100000"));
static int minOverlap;
static {
// An overlap of 1 or more is allowed as an overlap.
// Increasing this reduces the overlaps between variants and peaks which are large.
String smin = CLI.get("MIN_OVERLAP", "min.overlap", "1");
minOverlap = Integer.parseInt(smin);
}
/**
* Gets the intersection of the two objects. This
* is not designed to be run in an n*m loop, see above comment.
* However once you have two objects which might intersect, this
* can do the mathematics and return the Overlap which the correct
* fields set.
* a = p.s - v.s;
* a < 0 ? a = 0 : a=a;
* b = v.e - p.e;
* b < 0 ? b = 0 : b=b;
* bisectRange = v.e-v.s-a-b
* @param variant
* @param peak
* @return
* @throws OverlapException
*/
public Overlap intersection(Located variant, Located peak) {
int vs = Math.min(variant.getStart(), variant.getEnd());
int ve = Math.max(variant.getStart(), variant.getEnd());
int ps = Math.min(peak.getStart(), peak.getEnd());
int pe = Math.max(peak.getStart(), peak.getEnd());
// We rule out peaks of size 1
// This is in an effort to reduce the number of hits.
if (pe-ps <= 0) return null;
// This is the part that weeds out non overlap peaks fast.
if (ps>ve) return null;
if (pe0&&(ve-vs)>0
? (float)intersectRange/(float)(ve-vs)
: 0f;
Overlap ret = new Overlap();
ret.setPeak(peak);
ret.setVariant(variant);
ret.setIntersectRange(intersectRange);
ret.setIntersectFraction(intersectFaction);
return ret;
}
/**
* Get the base of the location which is used for sharding.
* @param loc
* @return
*/
public int getShardBase(int loc) {
return Math.round(loc/baseSize);
}
public String getShardName(String chr, int loc) {
StringBuilder b = new StringBuilder();
// Must have a valid chromosome for a shard.
final String chrGood = cservice.getChromosome(chr);
if (chrGood==null) return null;
b.append("_");
b.append(chrGood);
b.append("_");
b.append(getShardBase(loc));
return b.toString();
}
}