@Override public ExpandingArrayList<VariantDatum> reduce( final ExpandingArrayList<VariantDatum> mapValue, final ExpandingArrayList<VariantDatum> reduceSum ) { reduceSum.addAll( mapValue ); return reduceSum; }
@Override public ExpandingArrayList<VariantDatum> treeReduce( final ExpandingArrayList<VariantDatum> lhs, final ExpandingArrayList<VariantDatum> rhs ) { rhs.addAll( lhs ); return rhs; }
@Override public ExpandingArrayList<VariantDatum> map( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) { final ExpandingArrayList<VariantDatum> mapList = new ExpandingArrayList<>(); if( tracker == null ) { // For some reason RodWalkers get map calls with null trackers return mapList; } mapList.addAll( addOverlappingVariants(input, true, tracker, context) ); if( aggregate != null ) { mapList.addAll( addOverlappingVariants(aggregate, false, tracker, context) ); } return mapList; }
@Override public Pair<ExpandingArrayList<Long>, Long> treeReduce(Pair<ExpandingArrayList<Long>, Long> lhs, Pair<ExpandingArrayList<Long>, Long> rhs) { ExpandingArrayList<Long> nt = new ExpandingArrayList<Long>(); nt.addAll(lhs.first); int index = 0; for (Long l : rhs.first) { if (nt.get(index) == null) nt.add(l); else nt.set(index,nt.get(index) + l); index++; } return new Pair<ExpandingArrayList<Long>, Long>(nt, lhs.second + rhs.second); }
@BeforeMethod public void before() { empty = new ExpandingArrayList<Integer>(); initCap10 = new ExpandingArrayList<Integer>(10); hasOne = new ExpandingArrayList<Integer>(); hasOne.add(1); hasTen = new ExpandingArrayList<Integer>(); hasTen.addAll(Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)); }