Examples with Location org.molgenis.data.annotation.core.datastructures.Location used on opensource projects

Example 1 with Location

use of org.molgenis.data.annotation.core.datastructures.Location in project molgenis by molgenis.

the class MultiAllelicResultFilter method merge.

/**
 * Combine ALT information per reference allele (in VCF there is only 1 reference by letting ALT vary, but that
 * might not always be the case)
 * <p>
 * So we want to support this hypothetical example:
 * 3	300	G	A	0.2|23.1
 * 3	300	G	T	-2.4|0.123
 * 3	300	G	X	-0.002|2.3
 * 3	300	G	C	0.5|14.5
 * 3	300	GC	A	0.2|23.1
 * 3	300	GC	T	-2.4|0.123
 * 3	300	C	GX	-0.002|2.3
 * 3	300	C	GC	0.5|14.5
 * <p>
 * <p>
 * So we want to support this hypothetical example: 3 300 G A 0.2|23.1 3 300 G T -2.4|0.123 3 300 G X -0.002|2.3 3
 * 300 G C 0.5|14.5 3 300 GC A 0.2|23.1 3 300 GC T -2.4|0.123 3 300 C GX -0.002|2.3 3 300 C GC 0.5|14.5
 * <p>
 * and it should become:
 * <p>
 * 3 300 G A,T,X,C 0.2|23.1,-2.4|0.123,-0.002|2.3,0.5|14.5 3 300 GC A,T 0.2|23.1,-2.4|0.123 3 300 C GX,GC
 * -0.002|2.3,0.5|14.5
 * <p>
 * <p>
 * 3	300	G	A,T,X,C	0.2|23.1,-2.4|0.123,-0.002|2.3,0.5|14.5
 * 3	300	GC	A,T	0.2|23.1,-2.4|0.123
 * 3	300	C	GX,GC	-0.002|2.3,0.5|14.5
 * <p>
 * so that the multi-allelic filter can then find back the appropriate values as if it were a multi-allelic VCF line
 */
public Iterable<Entity> merge(Iterable<Entity> resourceEntities) {
    ArrayList<Entity> resourceEntitiesMerged = new ArrayList<>();
    PeekingIterator<Entity> resourceEntitiesIterator = Iterators.peekingIterator(resourceEntities.iterator());
    if (!resourceEntitiesIterator.hasNext()) {
        return resourceEntitiesMerged;
    }
    Location location = Location.create(resourceEntitiesIterator.peek());
    // collect entities to be merged by ref
    Multimap<String, Entity> refToMergedEntity = LinkedListMultimap.create();
    while (resourceEntitiesIterator.hasNext()) {
        Entity resourceEntity = resourceEntitiesIterator.next();
        // verify if all results have the same chrom & pos
        Location thisLoc = Location.create(resourceEntity);
        // at least chrom and pos have to be the same, ref may be different
        if (!location.equals(thisLoc)) {
            throw new MolgenisDataException("Mismatch in location! " + location + " vs " + thisLoc);
        }
        // add to map by ref, so we get [ref -> entities to be merged into one]
        refToMergedEntity.put(resourceEntity.getString(REF), resourceEntity);
    }
    // now iterate over map with refs and merge entities per ref
    for (String refKey : refToMergedEntity.keySet()) {
        boolean first = true;
        Entity mergeWithMe = null;
        for (Entity entityToBeMerged : refToMergedEntity.get(refKey)) {
            if (first) {
                // merge all following entities with the first one
                mergeWithMe = entityToBeMerged;
                first = false;
            } else {
                // concatenate alleles
                mergeWithMe.set(ALT, mergeWithMe.get(ALT).toString() + "," + entityToBeMerged.get(ALT).toString());
                // concatenate allele specific attributes
                for (Attribute alleleSpecificAttributes : attributes) {
                    String attrName = alleleSpecificAttributes.getName();
                    mergeWithMe.set(attrName, mergeWithMe.get(attrName).toString() + "," + entityToBeMerged.get(attrName).toString());
                }
            }
        }
        resourceEntitiesMerged.add(mergeWithMe);
    }
    return resourceEntitiesMerged;
}